The biggest elephant in the room for me is the presence of AI. If the peoples of the SW Universe can build thinking machines, then battle droids and droid starfighters should be the norm, not an outlier. If they’re concerned about a possible Skynet situation, then remote-controlled drones are a reasonable alternative. There’s no reason the Republic/Empire should default to clone/stormtroopers, and absolutely no reason they or the Rebels should use organic pilots. And just saying droids are inferior to organics doesn’t cut it, not when we’ve seen they’re capable enough in a warzone to get the job done.
As sci-fi, this bothers me. As fantasy, it doesn’t.
Yeah… that’s really difficult to explain. It’s one of those things that is hard to realistically address without killing the whole franchise. The only possible excuse available to explain non-droid armies is cost. You could claim that battle droids are just more expensive to manufacture and require more energy to operate. But Star Wars actually seems to do the opposite, making it seem like battledroids are cheap, mass-produced crap that are inferior to clones. (Although Andor claims human prison labor is somehow cheaper than droid labor.)
As for biological star-fighter pilots, yeah, there’s pretty much no way to explain that realistically. It’s one of those things that just has to be accepted in order for the franchise to work, along with sound in space and hyperspace travel. (It doesn’t help that Star Wars calls attention to this problem by actually showing computer-piloted fighter craft in the Prequels.)
But I think adding in sci-fi elements as much as possible helps to establish boundaries and limitations that can help make stories more interesting. Like for example, there should never be large Napoleonic-style ground armies - it’s so ridiculous and creatively bankrupt. (I always wondered why in Phantom Menace, when the Gungan army assembles out in the open, the ships in orbit don’t just immediately nuke them.) At least in the OT, with the Battle of Hoth, they really put effort into explaining why the Empire has to deploy ground forces. (Although admittedly the design of AT-ATs is hard to explain realistically).