I'm sure making the jump from isometric to full 3d was a gargantuan hurdle, but I still don't understand why the story took such a hit. With only a handful of details to alter for the ending, you are essentially forced to side with the brotherhood and follow in your father's footsteps. Like you can be an asshole and poison project purity but it hardly changes how the game plays out. This is the main reason I like it less than NV and 4.
The setting and world are excellent. Much more desolate than the following games in the series and i totally understand why that appeals more to some people. I just don't think the story or characters really have the chops to contend with New Vegas.