Having played the old Fallout games as well as Fallout 3, I'll list what I would like to see implemented; since everyone is doing enough "better quests"/"items and ideas" for me.
I would like to see better character creation. Not the physical look of your char (that was perfectly fine as far as I care). I mean the stats and such. In Fallout 3 your character was pretty much God by level 20 (hell he/she was God before that). There was little point in trying to make a specified build for your character since it was so easy to become a jack-of-all. It was just really up to you on how you wanted to kill your opponent. Tagging skills didn't really mean much since very little was really determined by your skill level. All locks and computer hacks just required your skill to be high enough. Another problem I noticed, were the books. They could be found everywhere, hell you could find 1-3 in almost every building! I'm not bashing Bethesda on this, since this was their first time making a game like Fallout, but they should definitely work on improving this.
For example,
Sneak Make the Stealth boy reusable, but determine how long it works and how well based on your sneak skill level.
Combat Skills Combat skills should be 1/3 per level. By that I mean it takes three skill points to raise your combat level by 1. This makes choosing the weapons you specialize in more meaningful, rather than just maxing them all out and being "Master Gunslinger of the Wasteland".
Traps This skill was combined with Explosives and Repair. In the old Fallout games it determined your ability to detect traps and disarm them. This skill should be brought back. The best way this could be utilized in Bethesda's game style would be to add a small hazard icon that appears when you are near a trap. The alert should be based on your perception and traps skill level. A low perception or trap skill level means you are less likely to notice a trap or the odds in which you are able to disarm it.
Repair Repair should be like Combat skills only instead of 1/3 it should be 1/2. It should also be more in depth allowing you to fix specific parts (like how you heal crippled limbs with stimpacks). With a high repair skill you should be allowed to utilize different means to repair weapons. Such as using a metal pipe to replace the barrel, oil to clean your gun, or as the game already allows, using a duplicate of the weapon to repair it. For bladed weapons, being able to replace the blade/hilt or to sharpen a dull edge. Things like sledge hammers should be even simpler with just having the option of replacing the head or shaft.
With things like these your character build becomes much more immersive and would increase replay value even more since your character build would have to be specialized in order to survive. As for perks, I'm conflicted. I like being able to choose one every level, but their bonuses are just too powerful and have virtually no consequences. This contributes to making your Fallout 3 character overpowered.