My working theory is that, in Fallout 3, Auntie Beth didn't have enough time to ruin the game. Or maybe they still had some competent folks around. Maybe these people refused to bow to Godd Howard, later on. Yeah, it was a good game. I actually played New Vegas first (b/c I couldn't get F3 to work), and had the same ''special connection'' feeling you have towards F3. First time through it, though, it felt too linear (I'm still of this opinion), and had none of the intricacies I had become accustomed to in New Vegas. This shock made me shun F3. I gave it another chance and found a great game... but it takes some patience, since its world is so fragmented. I mean, you can play through it and miss some very interesting side quests and places which are like tiny islands of goodness, lost in Wasteland DC, possibly more interesting than the main storyline.
On F4, it has often been repeated... it may be a good game, depending on what you're comparing to. It's just not a good Fallout game.