The top three things I would like to see:
1) Blueprints: The ability to create an exportable/importable blueprint of a structure. This would allow players to share their creations with others as well as move their own favorite buildings between worlds. Sims has something like this, and it's very popular and does a lot to add to the community. If it feels too much like cheating, the blueprint could only be activated if the player feeds it the mats.
2) Paint: Dye is cool and all, but building my house out of flammable mats just to get colors kind of sucks. Alternately, just make dye work on different mats (stone, cobblestone, wood planks, glass)
3) Moveable spawn: People are always going off on the Minecraft forums about how people should explore their worlds. The biggest inhibitor for me is finding my main base again if it's 2-3 days away from spawn. I end up starting a new world, building a small base, gathering mats, then exploring slowly outward while building beacons and wayshrines until I find a good location for my main base. This is very time intensive and gets old after a few worlds. I would explore a lot more if I could take the bare minimum for survival with me and move my spawn point at will.
To the "there's a mod for that" crowd: finding these mods, installing them all, and praying they all play nice with each other is a major deterrent to enjoyment. It also makes it much harder on the more casual crowd that would just like to play the game without spending hours on forums. This is compounded by many of these mods (like Cartographer) being external programs and not usable in game.