Some people don't like 3D, because it doesn't look like 2D, in original fallout, even if you'll make less smooth animation, make it more "pixeled", etc. still it'll be 3D, and 3D isn't 2D. It'll be something new, those people who never played fallout before and, don't really know why, are playing FOnline playing it for thier reasons, they won't care about 3D, and those who played before and now playing FOnline for the same reason as 1st mentioned people, won't care about 3D too as they're playing FOnline without caring about fallout. If people are playing FOnline because they want to play fallout and fallout isn't more interesting for them much, they will care and won't like 3D.
Other people are saying that it's not fallout anymore, as it's not rpg, you can't play your role in some storyline, you can't be thief, lockpicker, tribal or hunter, if you'll "try" to roleplay, it'll look ridiculous here in FOnline. Roleplay possible when you're, usually friends, co-operative completing usually single-player campaign in some rpg game where each of you playing some role in "party" and doing thier actions based on thier aligment/class/whatever or whoever you RPing, choosing thier dialogue options and doing needed actions through whole game. It makes you feel as how you would do actions in that world if you were that character. In arcanum co-op mod you can roleplay dwarf who likes to drink, elf who doesn't like dwarves and technology, or a thief robbing stores at night who will have problems after and other players (as they are one party) will have to do something with it (usually it ends with slaughter whole town, but oh well...). I can't imagine roleplaying in mmo where all actions are player based, if you're RPing in place where are only players, you, probably, doing something wrong, as it's easier to live in real life and talk with people there. So those people (who are saying it's not fallout anymore) don't care if it'll lose something from original fallout as it's not original fallout long time ago and they're playing it as other game.
This way 3D will be disliked by people who wanted to play fallout but with other people, not alone in singleplayer with the same story over and over that they know. And there's nothing can be done, if only 3D will look very very very very very similar to 2D without adding other things, but then... why do need to make it 3D if it'll be look like before without changes? Those people don't need long hair dudes or bald dudes or running supermuties or pinksuits or brown CAs, character description on binoculars will be enough and ability to play some role in game and good old 2D sprites from fallout.