Let's see... I agree about Doom 3. Although Doom 1 and 2 were simpleton shooters with no memorable story whatsoever, Doom 3 topped it off. Open a door, shoot to kill the enemy waiting behind it. Step into the room, wait for the lights to get turned off, shoot in the corner to the left of you and behind you to the right to kill the two monster spawns. Repeat. Seriously: The game was fun for about the first one or two hours, after that it was incredibly boring.
Oblivion definitely killed Elder Scrolls. Procedurally generated landscapes and dungeons simply mean death for every serious RPG. Add level scaling applied to the complete world (every monster you face always matches your level. If necessary complete monster types get replaced by bigger monsters) and you get the abomination that is Oblivion. That thing isn't an RPG, it's a simpleton hack & slay with no risk of dying other than utmost and sheer stupidity. I don't need an ultra-hard game to enjoy it, but it would be nice if I get punished for approaching, let's say, a lich when I'm only level 5. Those things are supposed to be hefty and I
should die when I try to attack it with a rusty butter knife. In Oblivion that supposed lich simply matches your character's level and falls apart because you looked at it too long. Basically, Oblivion's main problem is that there is no challenge in there. The world feels stale and completely generic, also partly due to the complete lack of any dangerous areas, but mainly because of its "random generator" roots.
Most adventure series died during that nonsensical transition to 3D. Monkey Island, Broken Sword, Simon the Sorcerer, Gabriel Knight, Sam and Max and so on... all turned 3D, all sucked compared to their predecessors. But hey, at least they're three-dimensional while doing so.
Deus Ex 2 "killed" Deus Ex, although I have high hopes for DX3. DX2 on its own wasn't really bad, but it just had no way to keep up with the first one.
Fallout 3 will probably kill the Fallout series, as Bethesda is doing it and they once described it as an "Oblivion with guns". So, they were either completely drunk while making that statement or they simply don't get the masterpieces that Fallout 1 and 2 are. Either way, it doesn't shine a good light on Fallout 3 for me.
Oh, yeah... and Gothic 3 showed how you kill a series with a bang. Really impressive fail. Visually very appealing world that makes you really
want to like the game, but bugs, balancing issues and a really really tiny story convince you otherwise. Sad thing.
PS: Oh, and how exactly can Quake 3 Arena be an Unreal Tournament rip-off? Both were released '99, so basically id would have had to spy on Epic to rip UT off. Still, I think Q3A killed the Quake series. I like Q3A, but it turned a single-player game with some story and a great multi-player into a multi-player only game, completely neglecting the single-player portion and thereby disrupting the series. Quality-wise, Quake 4 killed Quake.
