Yahtzee mentioned that "when I said 'sequels' I meant ones involving the same characters". In that case, Bioshock 2 and Assassin's Creed 2 are on the borderline, since you play with different characters and fight different villains, or am I wrong here?
In my opinion, with the exception of a few rare games that really bring out something new, we've been playing sequels (sorry, 'clones') of games from the 90's for too damn long. Some have improved on the formula. Assassin's Creed is the worthy successor of Prince of Persia. Why on earth would they still release Prince of Persia games without the open world idea of AC is beyond me. I can dig remakes of older games, such as Tomb Raider Anniversary, to the extent that I can't figure out why they took time to make Deus Ex Human Revolution from scratch, instead of remaking the original. There are sequels which I would love to play (if done right), such as a No One Lives Forever game, a Sim City or Transport Tycoon. I'd love to see a good Pharaoh successor, or Rome Total War remade with current graphics. I for one can't wait for Skyrim and I pray to the gods that it's more like Morrowind than Oblivion (fat chance tho). Or Heroes uhmm.. (which one is it?) and pray that it's as close to Heroes 3 as possible. I've been praying to the dark side for years to get a Jedi Knight game (not that console port crap they did) or an I-War 3. Or Thief 4

And look, Metal Gear Solid 3 was a joy to play and had probably the best spy story ever told. Sequels aren't bad... it's the choice of what's turned into a sequel and HOW they 'sequel' it that is. Let's all be honest and just say what 'sequels' we hate to see.
Fifa (and all other sports games): an update roster every year and better graphics wouldn't be BAD, but the changes are so small that you're better off buying one at 4-5 years interval.
NFS: it's been bad ever since they made the good one: Porsche Unleashed. They've been toying around with other stuff and Underground 2 was fine but they just stretched it out too much. They stepped on GTR's turf and got smoked for it. Unless they come back to the "one brand history" type, they'll just continue to waste time and money. We're bored with NFS and have plenty of better alternatives.
Final Fantasy: been good for a long time, but Hironobu Sakaguchi left just after releasing his masterpiece (FF9) and it's been steadily going downhill ever since. FF12 was fine but they abandoned the concept too fast. From "I can't wait to see the next title", most of us are now thinking "I wonder just how BAD the next one's gonna be".
Metal Gear: this 'thing' just won't die... The third one was splendid but the more they go into weird futuristic conspiracies stuff, the worse it will become. I wonder just how many entire minutes of play we'll have in the next one.
Call of Duty: I would forgive them if they simply made Stalingrad again. And again.. and again. And let me play the German side. Modern Warfare 1 was fine, but they've ran out of cake and now they're just releasing Fifa with guns.
Prince of Persia: just die! Die, you time rewinding freak! Pass your shit to flight sims where that trick would be really useful. I'm tired of having a broken column as my only possible path to save life on earth. Anybody here ever marveled at just how stupid architecture design is in PoP?
The rest (everything else that has a number next to its name): some are good, some were bad to begin with. Some are good for a while (like GTA, before GTA4), then mess up, then turn into something good (Red Dead Redemption). Others blow up their chance on the second title (Mafia).
It all sticks to a very simple formula: with few exceptions, games have become more and more shitty. The main reason is simple: graphics. Too damn expensive and take too damn long to make. Everything else derives from this simple truth. The problem with any sequel is basic physics: it's released some time AFTER the original. Thus, it's shittier, but with better graphics. Sequels are not the CAUSE of everything that's wrong with the gaming industry. Sequels are a symptom and, in unfortunate cases, a simple victim.