Personally, I would rather have deeper quests (and more of them) and more factions to join rather than choices in just about every quest. They already introduced more choice than usual in Skyrim and it didn't work out so well. Many people blame radiant quests for the lack of main story quests/faction quests, but I blame the significant choices that the PC can make, such as joining the Dark Brotherhood or destroying them, or which side wins the civil war. Basically, Bethesda have to work on alternative settings, NPCs, dialogue, scenery, etc. every time the player makes a choice, which not only makes the game more prone to bugs, but also takes away time that could have been spent fleshing out main/faction quests.
Don't get me wrong, I'm not against decisions like letting someone live or not, or even decisions like in Morrowind where you got to pick which Great House to join. I'm just against having massive choices and decisions which Bethesda are going to have to divert a lot of time and effort into, and would likely make main quests and faction storylines even shorter than they are in Skyrim.