I can think of several good ideas in Fallout 3 that I'd like to see carried over into the Elder Scrolls, here are a few I can think of.
More involving quests, with multiple options which will have noticable concequences, this doesn't necessarily need to be wiping an entire town off the map level concequences, but it should be something you will notice, and something that, if you knew of the concequences, you'd have to take into consideration. In Morrowind and Oblivion, quests rarely give you multiple options you can choose, and when they do, it's also uncommon for those options to actually have any lasting concequences.
I would also like to see hand-placed items that are not leveled and not quest related, and not just occasional pieces of food, clothing, or low level weapons and armor (a few places had iron or steel armor laying around.) I'd like to see things that you might still bother to take if you were in a higher level, and if you found them at a low level, you'd be very pleased of the find you made, this should also include unique items. In Oblivion, I was rather disappointed to know that the vast majority of unique items were quest rewards.
Having you actually choose from lines of dialog that have been written out, instead of just clicking on keywords and getting a response. Even if the end result is the same, this would at least make it feel like you're having an actual conversation because rather than choosing "rumors" your character would instead ask "Have you heard any interesting rumors recently?" or something like that. This could also be helpful for role-playing, as you could get multiple dialog options in the same conditions that reflect your personality. Of course, NPCs should respond accordingly, it could also be tied into disposition, if you're rude to a character, that character should like you less.
More violent combat, though not on Fallout 3's level. When my enemies are killed from being repeatedly chopped by an ax, they should be wounded appropriately. Fallout 3 was a little too extreme, as I said, things like exploding heads would just feel silly in the Elder Scrolls, but combat in Oblivion just wasn't brutal enough.
I'd also like to see location damage, not necessarily "If you get hit in the head, you die." type location damage, but if you get hit in the head, you should take more damage, and maybe you will die if you don't have enough health or the attack is powerful enough. Crippling limbs is not needed though.
Realistic facial hair, and not just as a feature only a single NPC who has his own unique, unplayable race has (like Sheogorath in Shivering Isles, whose beard is a unique feature of his unplayable race.)
Dungeons that made sense, in Oblivion, the dungeons weren't always bad as dungeons, but if you actually think about the fact that they probably weren't originally built to be dungeons, and that most of them are ruins of ancient forts, Ayleid cities, and such, they really don't seem to make much sense. Morrowind did this better, but the rest of the Elder Scrolls series also applied it. In Fallout 3 on the other hand, the "dungeons" were often abandoned buildings like schools, hotels, offices, and such, and you could often see evidence that, before they were nuked and became lairs for mutant animals, feral ghouls or super mutants, they actually served a practical purpose, you could see beds, chairs, bathtubs and toilets, you could find rooms that actually had a function, and sometimes this was incorporated into gameplay, like being able to unlock doors by hacking a computer or finding items that seem appropriate given the building's function. While of course, the dungeons themselves that were used in Fallout 3 might not fit into the Elder Scrolls, I'd like to see Bethesda apply the same philosophy when designing them, and think about what purpose the dungeon was originally meant to serve, and how to reflect this purpose in its design.
As for things I wouldn't like, here are a few, one must keep in mind that these are not necessarily things I didn't like in Fallout 3, some of them are things that worked well in Fallout 3, but I don't think they would be appropriate the Elder Scrolls.
VATS, or a similar system. I actually liked the VATS system, it brought in an element that is generally not present in first person RPGs, but I don't think it would fit the Elder Scrolls series. Fallout started out as a series of turn-based, isometric RPGs, but when Bethesda picked up the license, they decided to make it first person, that's fine with me, I'm not against change in games, if one developer picks up another's license and decides to try their own take on the game, I'm perfectly fine with it, and I would gladly play such a thing if I liked the direction the developers decided to take it in. However, I believe that the roots of VATS are in that transition, it appears to be an attempt to bring an element of Fallout's original turn based combat into Fallout 3's first person real time combat. The Elder Scrolls, however, was first person to begin with, and I don't believe such a thing has any place in the game.
Experience based leveling. Skill based level progression as in the Elder Scrolls is a feature that sets it apart from other RPGs, I don't want to see it sacrificed.
A small amount of armor and clothing slots. Considering all the aspects Bethesda carried over from the Elder Scrolls into Fallout 3, I was quite disappointed to see that this one didn't make it in, granted, a few armor and clothing types in Fallout 3 really had no business being in separate pieces anyway, for example, a radiation suit needs to cover your entire body for it to be very helpful, I'd think, and power armor probably needs all parts of it to really be anything more than really heavy armor, but some armors in Oblivion are single piece too, for the most part, though, I'd actually like a return to Morrowind where there were separate pauldrons and gloves and gauntlets were divided into left and right pieces, and such, rather than even fewer slots than Oblivion has.
Onto the subject of unique items again, no "unique" items that look identical to normal items, unique items should be like the Daedric artifacts and such, they should have a unique appearance, if they're really not important enough to have a unique model, Bethesda should at least give them new textures like many quest rewards in Oblivion.
A definite ending after which you cannot continue playing upon completing the main quest. Granted, most games have this, but I hope the Elder Scrolls never becomes one.
The karma system.
A lack of joinable factions, this was alright for Fallout, but for the Elder Scrolls, it wouldn't feel right without several factions to join.
Oblivions infamy svcks! It's a two sided system, a good/evil measurement that gives you penalties that you don't care for even if no one knows you did it.
Fame/infamy is in no way a good/evil system. It is not an omniscient metaphysical concept that enforces objective moral guidelines, it's your character's reputation. To demonstrate, killing people in the Arena gives you fame, then is killing people in the Arena good? These aren't bandits and criminals you're killing, sure, maybe some of them did do bad things, but you don't know, for all you know, they could be perfectly decent, law abiding citizens who just decided that they could make a few septims by fighting in the Area. And yet you slaughter them without mercy, all because someone pays you to keep the crowd entertained, and if you don't kill them? They kill you instead. Then we have the Thieves Guild, granted, it's definately
illegal, but the Thieves Guild is against murder, and one could say that it's closer to the common portrayal of Robin Hood than ruthless, merciless thugs, yet doing Thieves Guild quests still gives you infamy.
Im also pretty sure the ES world is supposed to be more or less moralless lol.
Not moralless (which seems to be a made-up word.) characters still have morals, and follow these morals, and judge their own and others' actions by them, what you want, I think, is "morally ambiguous", as in it's not always clear who is wrong and who is right, you don't have one side that is obvious and completely good, and one side that is unquestionably evil, instead, you will have multiple sides which are often all good, according to their own personal definition of good. In other words, instead of simple battles between obviously evil villains who are evil simply for the sake of being evil, know they are evil, and are still evil anyway, you have battles between two sides which each might have points that make sense if you stop to think about them, but you still have to fight them, because the other side's point isn't compatible with that of your side, or because the means they use to achieve their ends are too extreme to be justified.
No, less gore. Oblivion is an rpg, not a shooter.
That has absolutely nothing to do with anything when it comes to violence and gore. In real life, if people die, whether by guns, swords, or other weapons that will cause serious bodily harm, it can get messy, if fiction has any pretenses of realism and shows deaths by such weapons, it must reflect this, or it will quickly lose its supposed realism, it has nothing to do with the genre of fiction. In Oblivion, it always felt silly that I could chop someone up with a large ax, and there wouldn't be a scratch on the body, the same went for Morrowind. Not showing blood and gore is a good way to keep a game or movies rating lower or get a TV program which features lots of fighting past the censors if it is to be showed on a family friendly timeslot, but it's hardly good for creating a realistic work, unless all the deaths are caused by something that audiences could reasonably believe would not result in much blood, or the camera is placed so that you won't actually see the wounds in order to hide the fact that they don't exist or aren't as bloody as they should be, but with its first person perspective and use of weapons that should definately draw blood, the Elder Scrolls doesn't have that advantage.
Plus, the Fallout series has always had very gory death animations, yet it's still regarded as a classic among RPGs, so much for the ridiculous "RPGs should have http://tvtropes.org/pmwiki/pmwiki.php/Main/BloodlessCarnage." argument.