Realistically, the Star Wars canon has no good concept of time. When the Tales of the Jedi period was conceived of, the writer (Tom Veitch?) I think just chose some random number that sounded like it was "a really long time ago." This is an instance of the classic Sci-fi/Fantasy writers have no sense of scale trope, IMO.
Given that, you have to kinda judge the TotJ/KotOR/TOR world through the lens of the writers not really comprehending just how much of a stretch of time they're working with. Whether it's technology (really? ships changed that little in 3,000 years?) or simply aesthetics, it is easier if you pretend this period in Star Wars history is really more like 200 years before the films rather than 3,000.
Having said that, I do agree that the aesthetic they chose for a lot of things corresponds a lot more to that of the films than the TotJ comics. Really, though, this criticism applies as much to KotOR as it does to TOR, though (FWIW).
I do kinda like the idea that the Galactic Empire was borrowing imagery from an old, legendary Sith Empire (e.g., the Imperial logo, the appearance of Star Destroyers), a la the Nazis seeing themselves as descendants of a long tradition of German Imperialism. (Not that the latter manifested in Nazi imagery so much as their ahistorical propaganda.) Granted, this isn't ever stated in any SW canon, but I like the idea.
Yeah, all Bounty Hunters are Boba Fett—this would "work" if Bounty Hunters were Mandalorians, but they're not. Worse, IMO, was the idea of making the Han Solo/Lando Calrissian archetype into a whole class. TOR isn't the first offender (KotOR for example had the "Scoundrel" class), but I've never gotten the obsession with this. The Imperial analog, the Agent, is so much cooler, and having the Republic version be an SIS Agent or Scout (to borrow a KotOR class) would've been a much, much better idea, IMO.
Again, the sense of scale thing rears its head. But if you look at some real royal lineages, some of them continued for hundreds of years. Famously, the Habsburgs of Austria (and Spain), for instance. They were Emperors of the Holy Roman Empire in 1273 and good ol' Archduke Franz Ferdinand whose assassination kicked off WWI 641 years later was heir presumptive to the Austro-Hungarian throne, descended from a branch of the same House of Habsburg. It's not unprecedented.
Completely agreed on this one, but I'll mention another pet-peeve planet for me: Tatooine. Tatooine is supposed to be a backwater dump that no one would ever want to go to and that nothing important ever happens on. And yet it comes up in Star Wars over and over again. Even George Lucas pulled this when he made Anakin from Tatooine. It's absurd.
Well, it's hard to say where the idea to use Hoth and Tatooine (for instance) came from, Bioware, EA, or LucasArts, but regardless, LucasArts should have nixed the idea. As stewards of the Star Wars franchise in gaming, they do a pretty terrible job with the canon.
Still, love the game, and it at least takes a dump on established Star Wars canon far less than some other games (or than, say, WoW does with Warcraft lore).