I'll make my first post here as this is a topic I'm very keen on
1 - I agree with those that have said the combat system needs to be greatly changed. As said before, it becomes to easy after about lv 8 even in difficult mode. Making the targets harder to kill, ie; shooting them more times, doesn't fix this problem. Yes there should be tough enemies like Overlord SuperMutants and such that are incredibly resiliant to gunfire etc as well as easy picking like mole rats and so on. FO1 got the balance right I believe in that early in the game the critters were not too hard to bump off but if you went out and into dangerous territory, you got splattered.
2 - More dialogue options and above all - MORE VOICE ACTORS! Come on, it can't be hard to hire a few more Voice Actors to play specialised NPC's can it? It got a bit tiresome listening to the same actors modify their voice for when they did the dialogue for different NPC's.
3 - A much bigger sandbox map with realistic distances. Also settlements and fixed encounters need to be spaced apart to encourage exploring.
4 - More & varied weapons. I want to see home made guns like muskets made out of steel tubing, crossbows and compound bows, slingshots, spears and javelins and hell, even rocks! Lets face it, guns in 200 years plus will be rare as hens teeth and as such the world should reflect this that why X-bows etc should be common and firearms [modern] are rare. And energy weapons even rarer although this will go against the canon of FO I think? It just irks me to see hundreds of energy weapons floating around in FO3 when it's 200 years since they were last made
5 - I'd like to be able to use vehicles and animals for transport. This would circumvent having to walk everywhere and nerf the fast travel mode. It'd also mean you'd have to mainain your animal/vehicle etc and they could be killed destroyed in a fight. This would add a great new element to the game and make players think carefully about riding into a firefight if they know their car or horse could get shot to pieces
6 - Better companion NPC's. I like having back up in certain fight and the NPC's in FO3 were amusing but they got rather stale after a time. They need more dialogue and should respond to situations like them telling you to bugger off if you are taking on something far too tough or putting them in danger. They diffinently need better AI.
7 - I like what has been said about New Veags' hard core rules, especially about ammo actually having weight! This should be mandatory, not hard core. Also limit the number of weapons you can carry, ie; 1 rocket missle launcher or large weapon, 1 rifle sized weapon, and a few hand guns. Otherwise, even though you have the carrying capacity, its ridiculous to imagine a person running around with a missile launcher, mini gun, fatboy, chinese assault rifle, laser rifle, sniper rifle and so on which with a half decent STR you could easily carry.
IRL, you would fall over and running?!
No way in hell with all that gear on your back! It just has to be a bit more believable. Less is more!
8 - More areas within settlements/places to explore. someone mentioned earlier Rivet city being a few decks and I agree, it was not enough for the size of the place. Also more ruins and less [intact] buildings. After 200+ years of negelct, most buildings would be rubble and that's not counting blast damage from A-bombs etc. In NEw Vegas though, since it never got hit and has had power via the Hoover Dam, I can see the city being moderately in good shape thus I suspect most of the places will look a bit like Tenpenny Towers, in fairly good condition. However, out in the wastelands, there should be hardly any old structures left standing and those that are have been repaired [often badly] by survivors who aren't qualified builders or engineers thus are likely to look like ruins.