So what's on everyone's wishlist? Here's mine:
Nested prefabs
Upgrade to modern Mono
Polished official solution for serializing and saving/loading full and partial gamestates
Shouldn't need a ton of work from Unity, or any changes in Unity's guts, but I think it would be immensely valuable. The idea would be to establish a sane standard and guidelines for the users to lay out and label their data suitably, and helping even beginners to do it. Plugin/middleware/asset makers would then also make their wares directly compatible with the standard Unity way. I recognize game saving and loading is fundamentally not one-size-fits-all, but they'd easily cover 90% of the use cases out there, and many of the remaining games that need custom stuff would find it easier to adapt to an existing system than to reinvent everything from scratch. It's important to be able to save either the full state (as in suspend/resume, or for debug purposes) or a limited amount of state for a normal savegame in the same project.
De-emphasize scenes
Begin a transition to where "scenes" are just one way of many to group, load and unload parts of the game world - essentially, big prefabs. Make dynamic, generated or piecemeal-loaded worlds equal citizens. I think simply having nested prefabs would let one get pretty far to this direction. This obviously goes hand in hand with the serialization and structuring of game state data. In the short term, as long as they stick to the scene-based system, I'd like to see its usability improved. Let me designate a default scene to open when the Unity project opens. (Which reminds me: give me a .unityproject file that opens the project instead of having to dig into Assets/Scenes and guess at an appropriate .scene file.) Give me hooks to run global code at game launch regardless of scene, or at the load/unload of every scene, without having to sprinkle stupid empty script objects around.
