I'd say Fallout 3 is better then NV or Skyrim, primarily because Fallout 3 doesn't feel like a broken game whereas NV and skyrim do. Fallout 3 didn't need "re-balancing" to balance two different forms of combat where one was near useless.
NV had the best storyline, a fantastic and a more dynamic storyline with better implementation of factions/etc but else wise it's just FO 3 repackaged and it still had some of FO 3's zero day bugs/glitches which was a bit inexcusable, overall I think FO3 had better quests like tranquility lane and blow-up megaton. Also the fact you could rather literally skip half of the main quest line and the game was fine with it was another awesome thing, you just had to know where to go which you'd only know if you had already beat the game once.
Skyrim has the best gameplay and graphics, but by far the worst storyline and the quest lines do not have the pull that FO3s and NVs had.
The perks on all 3 are good but with FO3 and NV the perks were in my opinion better, Skyrim's perk trees are better then the flat interface that FO3 and NV had but Skyrim's perks themselves just aren't very well fought out. Also SPECIAL gave just basic humans more uniqueness against other humans then all 10 races have in Skyrim. That Said I believe it was possible to get 10 in every attribute in FO3 and 100 in every skill, tho it wasn't easy, requires a lot of work and really wasn't meant to be done.
EDIT:
lol fallout 3 is like RPG lite, you should play some baldur's gate or morrowind.
Fallout 3 might not be the most RPG of RPGs but the RPG elements around the storyline itself were more flexible and played out better then the quests in Skyrim just due to having a morality system. In Fallout 3 you could be a badass or you could be a hero/heroin and you decided that. Skyrim you do the MQ... kinda neutral/good, College of Winterhold, kinda neutral, Civil War again morality wise only neutral, Thieves guild neutral/evil and Dark brotherhood is kinda evil. So in fallout 3 you made decisions and you faced the consequences of those actions which is more RPG-like then what skyrim has in terms of storyline.