I can't decide, theres many good things about Fallout 3 and lots of bad. Personally, I hate VATS completely, but early in the game with very little ammo and dodgey "cone aiming" with normal fire so you can really hit where you aim its fairly unavoidable if playing on a higher difficulty.
But in general you don't know you shouldn't really stick with the main story line, i did what I thought was a lot of side stuff and still finished far to quickly. THe main story did need to be much longer and drag you around a LOT more of the side content.
I personally hate the addon's you get for things like oblivion. To much time spent making it moddable, then when you come in later on to play the game, you ask someone what you should install to make the game better and everyone tells you a completely different combination of things to install. YOu end up having no idea why its better, or worse, what you're making better, what you've screwed up, etc, etc, etc. I generally felt lost with Oblivion because so many people slated the standard version, and there was simple to many options to add into the game. I don't want to play through a long RPG 10 times to find the perfect way to play.
A game made by the designers thats finished, and made themselves with a story that incorparates most of the content is really the way to make a decent RPG, and you don't seem to get that any more.
FAllout 3 has probably been the exception of the RPG's in the past few years, I think both KOTOR's and Mass Effect were brilliant, with the later a little shallow and light on content, with too much of the side quest stuff, utterly irrelevant and generic but the best main story in a game in years.
I think maybe those 4 titles have maybe been the best for me as far to many are based in the "fantasy" world, and they all have orcs, and elves, and goblins and dragons in. The storys always end up being so similar and completely not original. The fact theirs 10 new big rpg's a year and 9 of them are fantasty elf/goblin type storys with the same sides being writen the same(when will we see one with elf's, man and dwarves being evil and the goblins and orc's good guys), is always going to mean overcrowded market of unoriginal crap.
I think what would help massively, would be a big break from the fantasy setting for a few years. Give everyone a chance to get over the concept, all try their hands at sci-fi and in 5 years when they go and start a new one they'll hopefully have a fresh take and not just churn out the same thing over and over.
Oh, I forgot, Fable 2 is pretty smegging good but is pretty heavily limited, not much in the way of character customisation and no armour's, limited range of weapons and so on, but made great by a really good story and characters.