First of all, hiiiii, long time since I've been around
Anyways:
top 5?
1. combat outside of VATS should be even more hampered by low stats (as opposed to less). This makes VATS more crucial, and FPS play style less effective (sniping with a laser rifle and 0% energy weapons skill is a complete design failure). Also, body part targeting with melee. I mean, how the hell did they mess that up?
2. Good facial animations and body language that help create emotive situations between characters (it goes a long way, and doesn't even require them to be good at writing!). A shortcut, perhaps, but it could help, as in many games this helps artificially expand on character memorability. Mass Effect 2 would be a perfect example of how this could be handled.
3. More consequences. Just plain more consequences. Consequences in economics are known as 'opportunity cost', they define the secondary (and sometimes most important) value of choices. A choice is defined by two factors... what you gain, AND what you now CAN'T gain. Without both aspects handled robustly, the choices will always ring hollow. As for the choices, please please PLEASE un-simplify them. Moral ambiguity much?
4. More expansive importance and implementation of statistics and SPECIAL, above and beyond what as been done in any Fallout. Obvious examples include retarded dialogue, but this also includes, for example, new target locations in VATS as your skill in doctor/first aid go up (it would be awesome to be able to attempt a kidney punch if you have enough doctor skill and perhaps the Anatomy perk). A natural bonus to energy weapons when your science skill is increased. Limb damage should be FAR more severe, stuff like that. This complaint has some overlap with my #1 on this list.
5. lower quality equipment drops, increased lighting effects and weather, weapon mods, armor skill stats, possibly the merging of energy weapons and science skills (energy weapon usage should be a mix between your science skill and relevant small or large guns skill), varying degrees of ability to see in the dark (with night vision and thermal vision and all that), and a million other 'small' complaints. Just, generally, more expansion of the things that Bethesda seems to focus on, as they seem to have a knack for presenting new ideas (even if they suck at preserving old ideas). If you're gonna ask for stuff, it might as well be things that you think might happen. Right?
This post feels a bit disorganized, but expanding upon it sounds like a job for an essay, and I have a school essay to write right now