I think we can all agree that FFG has made an *awesome* game, here. Heck, *years* into playing it, I'm still completely hooked and can't ever imagine that stopping - it truly captures the feel of Star Wars in a quick-playing experience. Heck of a lot of fun!
But...even so...there have been things that definitely leave one...scratching one's head, in trying to parse it into the lore of the setting. What have you guys found as the thing that just...may work fine from a game design perspective, but doesn't really make sense lore-wise.
Personal suggestion:
TIE Defender generics at PS1/PS3. Yes, yes, the TIE Defender has had to be re-imagined a few times from its deleriously-OP debut in 'TIE Fighter'...but one thing it has consistently held onto was the 'lore' background of being a fighter only flown by the elite and highly skilled. The pilot pool for the TIE Defender commonly stated as being drawn from the TIE Interceptor pilots who had managed 20 combat missions and survived. Consider that modern 'ace' status is conferred on getting three to five kills, we are looking at Royal Guard-level skilled Interceptor pilots (PS6 or better) being given the Defender, and...*plop*, back down to PS1. LOLwut? Sure, it's a "new fighter", but situation awareness is most of fighter combat, and that experience doesn't go away just because you've got better systems behind you.
Would definitely have liked to see both TIE Defender generics get +2 skill*, and the resulting PS5 pilot have an EPT slot, for their cost.
* So, sure, reflecting some decrease vis-รก-vis 'getting used to the new platform' unfamiliarity to start with.
Runner up:
Crew on ships. Aside from the small-base ships, pretty much *no* ship in the game has a believable number of crew. I mean, take the Millennium Falcon (please! *badum, tshh*) - we saw it spend most of one movie with Han, Chewie, C-3P0, Leia, *and* R2-D2 on it. Heck, the first time we saw it in a real dogfight, it was being flown by Chewie, with Han and Luke both gunning, and C-3P0, Leia, and R2-D2 doing their thing. 5 crew slots? And then that whole lot ALSO stuffed themselves into the cockpit, alone of an Imperial Shuttle in a later movie.
Of course, from a game balance perspective, I get why FFG limited the crew slots - crew "interesting enough" to be worth equipping one of in a HWK-290, TIE Phantom, or B-Wing...would be the same upgrades that could be insanely unbalanced if you could equip 5-7 of them in large-based ships. I think 'lore fail' applies, here, and it's a shame because FFG has since created the solution to it. As had been long hypothesized (and validated with the 'Raider' release) - if the idea of a 'system upgrade' had existed in FFG's mind when the TIE Advanced was released...it would have had one from the get-go. But that idea wasn't there, so it didn't. I think 'large'-base ships suffered a similar fate. They should probably have had no more than one crew slot (IF that), and instead introduced the concept of 'team' slots much sooner.

