I ran into a few headaches while trying to build a space shuttle and a rocket to get it into space that I feel are worth addressing. The first is that it is a a pain to build a shuttle in the VAB, due to the way symmetry works. I found it much easier to build a shuttle in the SPH but could not transfer what I had already built in the SPH to the VAB for the rocket building stage of development through the in game ui(I had to exit the game, move the craft file into the other folder and edit the .craft file to associate it with the VAB). Even though it is possible to move the craft to the other building this way if I ever want to alter the shuttle itself it's now a different ship and I can't easily move it back and alter the shuttle as I want to without bringing all the rocket stuff as well and see the center of balance and thrust etc.
It would be incredibly useful to be able to able to have a more modular construction ui where I can design something once and include it in several different craft. For example, I only really need 1 basic satellite but if its target orbit is kerbal or the Mun or something further I need a different delivery craft. I shouldn't be rebuilding the same satellite more than once. It would be really nice to have a satelittle save file and import it into each of the rocket designs as I build them.
Once I have enough craft the simple list is not really ideal for finding the craft I'm looking for. It would be really nice to have a folder structure that I could drop crafts into so I could have a folder for all shuttle delivery rockets, all satellite delivery rockets all atmospheric place etc. Even better would be to allow the player to add meta data to the craft save and filter the list of crafts.
When building the shuttle and rocket together it I have to launch each rocket stage individually starting from the last stage first in order to test the balance of the rocket because I can't see the center of thrust or mass for a individual stage once I start adding more stages on. It would be really nice to be able to select a rocket stage when adding those indicators in the construction mode. The center of thrust also assumes all rockets are firing, it would be nice if this could also determined by the a selected stage.
In summary:
Modular contruction design - build a complelx part, save it, import it into other crafts.
Move in an out between the contextual contruction modes in VAB and SPH, including moving crafts between the two buildings.
A Better UI and structure for organizing saved crafts, including meta tags, filtering and folders.
Select a stage when viewing stats based on center of thrust and mass.