It seemed to me that complaints against oblivion were rectified in F3.

so for skyrim, i think its safe to assume the following..

.no levelled scaling

.unique hand placed weapons

.more voice actors

.more fleshed out side quests (even more so in vegas)

.more unique NPC's with detailed backstory

.more followers that dont involve having to complete a guild

.less cut/paste dungeons

.a pet dog?

.less respawning containers, most shacks in F3/NV can be made into a home with safe storage.

.non walled towns, more settlements.

.a way of shortcutting the MQ

.way of changing appearance midway through the game.

thats all I can think right now, but I highly doubt they will omit any of these beneficial changes in TESV.

Well we can't really be sure of anything, mainly because the game is no were near to being released yet.

Comparisons to Fallout 3 can be tricky. For something like level-scaling it's a pretty safe bet - Bethesda acknowledged that level-scaling in TES IV was unpopular. This will probably also result in more placed items, rather than heavy reliance on containers. In both cases TES III is as much an object of comparison as Fallout 3.

Other things may be kept separate. For example, you could get canine companions in Fallout 1 and Fallout 2 which is why this was considered for Fallout 3. Bethesda might like the companion system enough to bring it over to the Elder Scrolls or they may keep it out specifically to help define the two different series.