Ok so there are many, many things I loved about Fallout 3, and some things that I didn't.
One of the things that I didn't - you have a MASSIVE sandbox landscape, full of interesting stuff to find and do. And while you're making your way across it, especially at the higher levels, you will be interrupted by scorpions or robots or raiders EVERY. TWO. GODDAMN. SECONDS. Also see: Oblivion, and every other single-player RPG ever made.
Seriously, random encounters should die a slow, agonizing death, alongside monsters that level alongside the player. (See "Oblivion", where the most challenging opponents in the entire game are the f--king goblins.) Why not give us a lot of set points where larger-scale encounters can be found, should the player want them? Instead of constantly being molested by minotaurs in "Oblivion" once you reach a high enough level, why didn't the game have "hard" areas, such as the spooooky forest which all the villagers would warn you not to go into because there was nasty ghoulies in there?
Another thing that should disappear: levelling with no visible signs of levelling. If I double my sword-swinging stat, I want the sword to be visibly faster and more powerful, capable of a lot more swings in the same time, etc. I don't want it to look exactly the same but get told that I've done more damage by some stat on the screen. I have Microsoft Excel for that. I want that sword to produce a more visible effect on the enemy - stagger them more, or produce more blood, etc - and LOOK like it's being swung with more force. I also want there to be a gameplay "benefit" other than just being told that it's doing more damage (and because the monsters level with you, this turns out to be a deficit anyway).
Soooo to recap this rather long-winded post:
1) Get rid of random encounters that just detract from the "exploration" aspect. Add encounters that you can (and must) plan ahead for, each one challenging and imaginative and different in difficulty. So if you're feeling ambitious, you can take on a minotaur king at level 1; and if you're looking for some easy XP, you can take on a cavern of goblins as a level 100 sorceror who can summon demon-lords at will.
2) Get rid of levelled creatures. There is NOTHING more annoying in "Oblivion" than being able to finally take on those damn goblins, only to discover that they're now all "Goblin Warlords" because the game arbitrarily decided that you were too powerful.
3) Make "levelling" feel as though it has an actual effect. If I level up magical abilities, I want my fireballs to be bigger and burn stuff for longer. If I level up bludgeoning weapons, I want them to be visibly more forceful. If I level up blades, I want them to swing faster and do more cutting damage, etc.
Seriously, is there ANY reason why this stuff can't happen, technically speaking, in a modern game?