First, both games took MAJOR elements out of the game (Where's my Vindicator minigun? WAAAAH) replacing them for nothing. No gauss weapons in FO3, no 'nades in TF2. Then they decided to revamp the whole gameplay, keeping some stuff here and there so the game wouldn't lose all of it's appeal to old schoolers.
Then, they sacrificed the humane feeling FO1 and FO2 had for a black and white, "Good guys are always nice and bad guys are always bad" kind of atmosphere. What happened to drug addicts greeting you and vault city inhabitants enslaving people? I can be a mean [censored] in FO3 if I want, but even if I'm a stealth killer, there will be some kind of aura around me which will tell people what kind of person I am, and what kind of stuff I do. Karma affects the game way too much.
Valve killed the immersive (alright, immersive is a strong word here) of Team Fortress with TF2. Back in TFC, they were just mean dudes fighting to death. Now they're charismatic, funny types. Bleh. Just give me my killing machine/vault dweller back. I don't want any "appealing" easter eggs (ZOMG, FAWKES/PYRO IS A GIRL!!!1!), I want Fallout 2's cheap humor, one of the elements which made it so great. I want to meet a farmer in power armor who only says "Oil Can", damnit!
I would write more of this [censored] complaint, but I must be boring you and/or going completely off the track. My points may seem trivial, but I'm sure a lot of Fo1/2 fans (And I'm not talking old schoolers only, I played fo2 for the first time last year) will agree. FO3, while being a great game, is just not the one. Hats off to Bethesda for making yet another great addition to my collection and for honoring black isle, but it simply just doesn't fit.
(Also, am I the only one who thinks VATS was only introduced in FO3 so it wouldn't totally lose it's old combat system?)