Ability to craft same looking armor with different materials. For example, craft Indoril armor or weapons with iron, glass, or ebony. That way end game armor/weapons wouldn't all be spiky daedric. You could ordinate throughout the land in some sweet black Daedric indoril armor.
Money pits
Have something to sink money into. For example, in skyrim you could of been able to buy Helgen, rebuild it, make the walls ebony, outfit guards in glass armor, etc. If ES VI is in Akavir,you could help defend towns from the Kamal through said upgrades and get sweet rewards.
Extinction / eradication quests
Kill all the vampires including the creator Mola Bal. Hircines been barking up the wrong tree too, let's have option to eliminate all the manbeasts.
"Boss" fights
The dragon priests were pretty sweet. Each had their own flavor. Should have more specialized/diverse fights.
Big change
Seeing the ash storms stop in morrowind was awesome. Seeing the red mountain explosion mid way through game and its effects would have been amazing.