This probably is too much to ask for, but I think the best way to do it would be 'astronaut programs'
IE you have the Mercury Seven(custom named program) and you use it thus:
Once added to the program a naut must:
get to 80% leadership, they need toget say 75% eva, once they reach this level they stop training. So you can simply add people to a program with certain parameters required and they train automatically to reach them.
Additionally you could still single out say one man for docking training(piloting?) if necessary, but these 'programs' could function as getting everyone up to the same minimum level of competence you want for a program, which is exactly what you want for training.
*IIRC this is not too divorced from reality, where they trained in 'groups'. Group one was the Mercury 7 I believe, then they had the next group and so on and they trained to develop their skills to the level they needed for the program they were going into, be it Mercury, Gemini or Apollo.
For example to my knowledge Alan Shepard didnt have greatly different training to John Glenn or Scott Carpenter. Other than the mission specifics like orbital testing jobs and whatnot.
(feel free to correct me if i'm wrong)
Thats EXCELENT IDEA - create own program with desired skills in this and that area, and they will train one skill after another until they reach desired levels.
And if you select for which space ship that program is (and slecting that ship tell you which skills are used) it will be great. If im not mistaken merury did supported eva, so it will be pointless to train eva for this programe.
And then we go for multi-crew ships which did have crew asigned to tasks (pilot, eva specialist..etc.
So selecting this multi crew ship it e.q. tells you crew 1 needed skills : piloting, learedship, crew 2 evan fitness, crew 3 piloting (lunar module :) ) , fitnes, eva..
so you will just throw your astonauts there, and then game put them to specific crew 1/2/3/4 (is 4+ crew ship even in game?) training nased on thier actual skills.
and expanding this to traing groups for enginers/ground controles is logical next step.
and it reminded me, pls add that training rockets gives some skill to human-raed rockets too (and vice versa), after all rocket s rocket, human rated just more fail saves.
and give player some incetive to run same program multipletimes, after lauching moon survey probe player have no reason to lauch if it is sucesfull, lets add that multiple lauchnich gives player some prestige and in some cases bonus to different type of missions. like mentioned multiple moon probes give moon landing expedition bonus to safety as you have covered multiple posible landng sites, not just one by one fly by.