The first thing that comes to mind is waiting for the first revisions of the Modding API. The reason for this is I don't want to have to keep fixing on going changes to Minecraft and keep things simple. I like the concept of their modding API and will be working with Mojang on their Jira site to offer what I can to the development of it. It also means I can give feedback directly to the developers, now that is pretty damn rare for most development companies.
Lets start with the basics, what do I want to create. I have spent significant time 'researching', which is basically playing the game, and thinking about what I could easily add to the game to give it some more spice. Of course most of this depends on how much power I get from the Modding API, but I'll outline some basics.
1. I want to add a few basic cooking recipes. Like Apple Pie, Meat Pie, Sugar Cookie, etc. This should be simple and easy to do. I expect these to be trivial to implement and would probably introduce me to some of the basics of their API.
2. I want to add another thing or two to farm. Maybe expanding upon my cooking concept I could add 'spice'. I'm even thinking maybe to add some alcoholic drinks and plants/items/blocks accordingly to make them. I would also add in a 'drunk' effect to the character I'm thinking something along the lines of what they do in World of Warcraft.
3. I want to improve trading, the current system feels clunky. It involves 'recycling' villagers to get the trades you want, there is little incentive to continuously farm certain items without having to keep renewing trades and other things. I know there is a ton of economy mods that exist in various ways, something with soft limits instead of the current hard limits would be better. As in, I buy an item, the price slowly goes up. I sell an item, the price slowly goes down. I would also scale items differently than the current ratios, they seem far to generous for diamond.
4. I want to improve fishing, the current system is boring. This would mean something like chasing the bobber, catching different types of fish, and a few other basic changes. Fishing overall should be more interesting, but just as it is in real life it can be fairly boring if you aren't catching them quickly.
5. More armor types, lessen the gap between items. Going from leather to iron, and iron to diamond, the jumps in power are insane. And in full diamond armor, unless you are playing on hard, you are basically untouchable. Even iron armor is pretty generous. I also feel there should be a few more tiers of armor, but I won't really go into those details. Ideally, a copper/tin ore and copper/bronze armor. I might add a tier after diamond called mythril, and make it incredibly hard to find. I would also be tempted to add silver into the game. Iron could be refined into steel and such. I am aware of mods which already do this, but I have a few other things I would extend this concept to.
6. Make armor more interesting. More RPG like. Currently, armor has a single purpose which is to reduce the damage taken by all sources. This is pretty decent, but because it only has a single role it has to be really strong to convince a player to make iron or diamond armor. Instead I would want to change it to have item affixes which add health, increase attack, increase movement, increase jumping height, increase tool strength, increase xp gained, etc.
7. More enemies/mobs. Currently, the number of NPCs in the game is pretty lame. I have a handful of enemies and a few passive mobs and a couple friendly. I know a few mods at different types of mobs, but I would also like to play around with my own version. Including mounts, guards, pets, etc. In combination with the previous idea, I would want to add factions, scaling enemies, scaling stats and other rpg elements.
8. More adventuring. The game currently is about setting up a base and eventually going to The End and killing the dragon. So after all that... then what? I'm thinking Quest-based systems with NPC villages, to gain reputation with various factions and earn rewards that are not possible in other ways. Quests which send you to other dimensions, get you to collect items, build things, send you to fight a boss, etc. The system would make the world feel more alive.
9. More item types. Tool wise we are in a pretty good shape, but armor-wise there could also be gloves, bracers, belts, rings, necklaces. More weapon types with different methods of attacking. The combat system could be overhauled to add in skills and a more complex battle system. Including staff's for magic and multiple ways to use the weapons. Spells/Skills/Abilities, etc could be in hidden tomes you find by doing quests, defeating bosses, and other difficult tasks.
10. Large-scale towns. Currently a village is a pretty simple concept, but what about expanding the idea to have larger places as well. With unique buildings and such, different types of guards, more rpg like and factions. Maybe even have 'kings' or 'leaders' which can be killed or allied with.
11. Large-scale combat and meta game. This is one of the largest concepts I have, which would be to literally re-create the Stronghold game in Minecraft. I've heard of other games being rebuilt in Minecraft and adding interesting twists, but this concept seems to be the most interesting but also the most complicated.
I have other ideas and such, but I figured I should lay out the basics. Obviously, there is no way I could do this list and as I descend the list things become a lot harder and more challenging. Of course, this all depends on what ends up happening with the Modding API. If I could assist with development of the API I would, but that is very unlikely.