Yes, Secrets of the Third Reich is technically "weird" WW2 with werewolves, undead and mecha - but I picked these games based on their similarities - both are based on Warhammer 40K mechanics.
(Also, I thought I'd already reviewed Chain of Command which is radically different than both - it turns out I haven't, though I kinda discussed it here.)
Bolt Action has a nice 250-page hardback rulebook with excellent production standards, with glossy goodness on a par with the very best quality rule books. Although quite a solid offering, SoTR's smaller softcover just doesn't measure up, with some hit-and-miss art. Both lack a thorough index at the back for finding things.
Winner: Bolt Action has shiny in spades
Initiative & Activation
Bolt Action is streets ahead of its 40K ancestor - you draw two colours of dice from a cup, and the player whose dice it is assigns that dice to a unit, with the face up side showing its order - you can choose Fire, Advance+Fire, Run, Ambush (overwatch), Rally, and Down (no fire, take cover, defence bonus).
In SoTR the top ranked officers "dice off" using their Leadership. The winner gets to choose who activates first, and players then take turns activating units, which is a bit more predictable than BA. Sergeants and officers have a "command range" and can issue orders Regroup/Form-up, Rally, Call off-board strikes or paratroops, ignore suppression, overwatch, and hold (save activation for later in the turn.) They can also sneak short distances to avoid enemy overwatch fire.
Winner: Tie. Both have pros and cons, but avoid the dreaded IGOUGO and are a distinct step up from their GW forebears.
Chalk and cheese? Or simply two different colours of chalk?
Shooting - BA
All bar the most inexperienced troops hit on a 3+, but I like how the "defensive save" is based on the quality of the troops you are firing at - a simple way to emphasize troop skill (and probably copied from Flames of War). Any shots that hit add "pin" markers that lower a units firepower and morale (as well as forcing it to "test" to execute orders it could normally do automatically.)
Bolt Action almost directly copies its ranges from 40K, accordingly rifles have maximum of 24", SMGs 12"and LMGs 30". This is a huge immersion breaker for me as it just "looks" wrong and out of scale in 28mm - a 1" tall guy shooting 24" gives a scale range of about 50 yards for a rifle. Yes, I know about "effective"ranges and how you need to "compress" ranges in some situations and some games, but this isn't one of them. Being able to stand 25"away from a fire team in the open, immune from enemy fire which is somehow plopping 1"short, is just silly, and a sign of lazy game balancing. (Leading also to the well documented example of how forces at each end of the Warlord's Arnhem Bridge set are immune to each others' fire).
Shooting - SoTR
Whilst weapons have "effective" ranges, SoTR correctly points out that most small arms range would exceed the games table and thus rifles and LMGs have unlimited range on the tabletop. Most shots hit on a 4+ , modified for cover etc like Bolt Action. The "save" is not based on the target's skill, but if they are wearing body armour (this IS a Weird War II game), though you could easily change this with a house rule.
Troops are not pinned but "suppressed" which means they move to cover and go prone, with penalties to firepower. There is a little more detail/complication when troops are hit - they can be "down" as well as being killed outright. Downed models can crawl about but don't contribute until tended by a medic. SoTR also allow units to lay down suppressing fire which don't damage but have a high chance of pinning down targets. Overwatch (reaction fire) also works more effectively than BA's rules. Winner: SoTR. Which is the "historical" set here? BA's Nerf-like weapon ranges cede it victory by default.
BA uses similar rules as for shooting, except their are no cover saves and soldiers usually get only one dice each (more if they have special weapons). Defenders who haven't yet activated can react by hosing the attackers with fire before they close in. Once in combat, attackers shoot, then defenders. The side with the most casualties is wiped out.
In SoTR both fighters roll d6 and add modifiers, with the winner scoring wounds on the loser, like 40K 2nd Edition. Terrifying monsters can really shred normal troops if they get in close. Unlike BA, the losers can fight on if they pass a morale test.
Winner: Tie. Both are simple and do the job they were intended for.
If a Bolt Action unit loses half its men from one round of fire, it must test 2D6 vs its leadership or be removed from the game. Units are also removed by losing close assaults. Units can collect increasing amount of pin markers which must be removed by pausing for a "rally" action.
Units in SoTR who take losses test 2D6 vs their leadership or retreat away from the enemy/towards their board edge. Units who are 'disorganized' can remove their status by pausing for a "rally" action.
Winner: Tie. Both pretty similar, in slightly different flavours. BA is more decisive/streamlined (a fail means eliminating the unit) and SoTR is more granular, but Bolt Action troops can collect pin counters.
Secrets of the Third Reich 'scales down' and handles smaller groups of troops quite well - here two British fire teams are ambushed by ghoulsArmy Builder
Bolt Action has a 40K-style force creation list and it brings with it the same meta-gaming mentality of cheesiness - particularly annoying in a 'historical' game. You really have to approach Bolt Action with the mindset that it is a 40K game with a WW2 skin rather than a genuine attempt at historical warfare. I won't discuss Bolt Action's balance issues here - I'm sure there's plenty of stuff on the net already about how things can be "gamed" - but even casually reading it I find it interesting that one faction gets a 17% bonus to moving shots for all its infantry: under difficult conditions this could mean "to hit"odds of 17% vs 3% for everyone else - i.e. 6x better. Even though they cost the same as any other faction's infantry. This is more disturbing given Bolt Action seems set on being seen as a "competitive" rules set.
SoTR is restricted only to set Weird War units, but given Bolt Action's casual approach to realism you could probably include a SoTR unit in Bolt Action and not notice the difference. It also allows for min-maxing cheesiness. However, a big shout out to its Vehicle Builder - which allows you to "stat out" any model in your collection or even make your own (handy for adding awesome T-43 or DUST mecha to your games.)
Winner: Neither, really - both systems can be "gamed". But SoTR gets the nod due to its versatile and fun vehicle builder.
Bolt Action appears to only have a half dozen but they're found in all the army-specific codexes. SoTR collects them all in its base rulebook, and its Doomsday supplement. Naturally, SoTR allows for a range of "weird" units like undead, vampires, mechs and werewolves.
Winner: SoTR - because there's less of them in the long run (and most are simply to describe the weird units - which is fair enough), and you don't need to spend $250 on all the
Bolt Action has pretty sensible and streamlined vehicle rules that are an extension of the infantry rules - vehicles can be pinned (i.e. reverse away from incoming fire) although armoured vehicles can ignore small arms. Scout vehicles can "react"to enemies by making a bonus move to escape (which seems pretty powerful). Shooting works the same as infantry, but hits on armour need to beat 7+ (making them impervious to small arms) - heavy weapons thus have bonuses to allow them to beat this. Shots can stun, immobilise, or set on fire vehicles as well as destroying them.
SoTR also has sensible vehicle rules that are an extension of the infantry rules (and even share the same table) - with small arms being unable to pierce armoured vehicles but sometimes luck out against very light armour or power armour. Shots that penetrate force the crew to pass a "bail out" Leadership test, and unlike the linear BA damage system hit locations are more detailed - you roll 2d6 on one of four penetration charts depending on where you hit the target - front, side, rear or turret. Mecha have their own charts. This is one area SoTR is distinctly more complex than Bolt Action. Probably a bit too detailed for my liking.
Winner: Bolt Action has faster, simpler rules which I prefer, though SoTR has more variety and an excellent vehicle builder.
Scenarios & Other Stuff
Premeasuring - SoTR says (and I agree) that wargames are not a depth-perception test (carpenters should have no especial advantage), and allows pre-measuring. Bolt Action makes you guess (which, given the very short range of rifles, means shots will be wasted, magically be dissipating harmlessly 1" from a target 25"away.)
Bolt Action comes with more scenarios (6) whilst SoTR has a measly three. BA also has specific artillery rules whereas SoTR allows commanders to call in off-board strikes.
Both games have nation-specific rules to add flavour i.e. SoTR Soviets may fire into friendlies in close combat, and their kommisars may fire on their own units to restore "discipline." In BA, Soviets get a free unit of inexperienced "cannon fodder"infantry but get to re-roll morale checks that would otherwise destroy the unit.
Winner: Tie. Both have pros and cons.
Secrets of the Third Reich's vehicle creation rules allows you to include awesome M.a.K, DUST and AT-43 mecha in the game...TL:DR
To compare it them 40K from which both descended: SoTR is 40K 2nd Ed, and Bolt Action is 40K 3rd Ed+.
This means Bolt Action follows the Games Workshop trend of excessively streamlined rules, sacrificing realism for quick "pick up"games. It also has nothing innovative at all as it copies all its systems directly from 40K or FoW (not surprising, given the authors). It's a quick, casual game, which uses mechanics derived from space fantasy with a WW2 "skin." The 40K-style army builder encourages cheesiness and gaming the "system" - which is sure to happen given the target audience of Bolt Action is ex-GW gamers. It also follows the Games Workshop routine of releasing "codexes" or army books which add in special rules for particular forces, some of which are more advantageous than others, and are more "gamey" than historical. This game is designed to encourage collecting different armies through "FOTM" codexes, and is aimed squarely at converting 40K players to historical games (which it does very well.)
Secrets of the Third Reich, ironically enough, is somewhat more realistic, given its "weird"focus, though its gameplay is also pretty simple and borrows heavily from 40K. It also has cheesiness, though this is somewhat more to be expected from an alternate-WW2 setting set in 1948, where undead, mecha and weird tech runs rampant. I feel it also "scales down" better - you could have a fun game using only a couple of squads - like the older style 2nd ed 40K and Rogue Trader. There is also only one expansion (Doomsday) vs the dozen or so army books available for Bolt Action.
Recommended: Since this is a "comparison" article I'll leave you to make up your own mind. That said, while I happily use SoTR for Weird WW2, for historical games, I'd eschew Bolt Action altogether: Chain of Command gives a more accurate depiction of WW2 as opposed to "space fantasy WW2".