There are a few upgrades to the game that I have missed for a while now.
1. Electric Propeller Engines - As suggested by many others, allows for flight on planets with atmosphere but without oxygen.
2. Fuel Hose - Module mounted on the side of a ship that allows a kerbal to pull out a hose that can be connected to other ships to refuel them. This would allow us to refuel ships on the ground which is vitually impossible right now.
3. Fuel Port - Small exhaust module mounted on the side of a craft. Allows you to jettison fuel.
4. Dynamic Fuel Tanks - Give us the ability to choose the fuel that a fuel tank holds in the VAB or SPH. The amount of specialized fuel tanks keeps increasing, even tough they have the same dimensions. Allow us to choose a dimension and then choose the contents. This will make the development of fuel tanks much easier for SQUAD since there will be no need for 3 different fuel tanks when a new dimension or fitting is introduced. The system could easily be expanded to allow internal fitting of batteries and other odd bits into a fuel tank.
5. Rearranged Tech Tree - The tech tree can be further improved. Many crucial items, like the ladder, is considered high-tech and isn't available early on.
6. Expanded Tech Tree - The tech tree is a very entertaining part of the game. I suggest expanding the tree with more nodes and fewer parts in each node. This allows the player to further customize their space program.
7. Improved Missions - The 1.0.5 addition to missions is a great start but there is still much work to be done on the missions available. There needs to be more diversity in the missions, especially the ones done on kerbin. The new improved aircraft parts are not properly utilized. A few suggestions would be: Pick up a kerbal on a deserted island, fly through checkpoints, pick up a package and drop it off at a certain place.
8. Redo the Part Constraints - The allowed part count of 30 in the beginning of the game is a little too much to pose a problem for the early rockes but causes too much problem just after the beginning of the game. I suggest another upgrade to the VAB and SPH that solves this problem. Starting with 20 pieces in the very beginning and allowing 45 afterwards before the 255 part upgrade would improve the gameplay without removing the interesting problem that it poses. The part constraint could also be an upgrade in the tech tree, which makes more sense and is more fun than spending money on a VAB upgrade.
9. Multiplayer - As more and more of my friends pick up KSP I really want to build rockets together with them. We want to build the WhiteKnightTwo and SpaceShipTwo and we can't fly it without being two people!
These are the things I miss the most in KSP!