I think one of the biggest problems is that we inevitably compare the games we play now to the games we played in the past. Nostalgia sweetens them, but really, going back and playing through them again, sometimes you can see the difference.
I do retro game from time to time, but I've found that, say, Half-Life 2 makes for a more enjoyable replay than the original. Why? Well, the original is a lot more predictable. Simpler AI, dumbed down "physics" engine that makes throwing a grenade a joke, etc.
I think one of the biggest problems we have lies in when we start comparing everything we run into to everything we've played before. I don't think it's such a bad thing that games can be derivative. Especially if they can present their derived works in a fun to play manner. Even in a case of System Shock 2 and Bioshock (as Yahtzee complained), I have to say, Bioshock was still an amazing game. Excellent atmosphere, excellent characters and good story telling, if a bit on the stupid-simple side due to the death mechanics.
Even if it was only just a more refined version of SS2, couldn't we enjoy it for that? Maybe replace the memories of SS2 with memories of Bioshock, instead of complaining that it was the same thing over again.
I mean hell, there will probably be someone complaining that Force Unleashed is just a dark side version of Jedi Knight, which was just a version of Dark Forces that had a lightsaber in it, which was just a clone of Marathon, which was just a clone of DOOM, zomg.
Here's to pitching TIE Fighters at massed phalanxes of stormtroopers.