[a little late to the party here, but bear with me, I'm new

]That's a very interesting idea! And amazing potential too, both for roleplaying and campaign opportunities.
Getting karma through training and getting karma through doing runs are very different things, so I would not worry much about giving out points proportional to time spent training. As for the skills themselves, I think the basic loadout would be [in SR4 terms] Athletics, Unarmed Combat, at least 1 more weapon skill for non-combat specialist, Pilot Groundcraft for everyone (so anyone can drive the car), Survival training with different specializations, possibly Infiltration, some Knowledge (Tactics).
Then added to that are specialist packages: Demolitions, Gunnery, Heavy Weapons, Pilot Watercraft and Pilot Aircraft. At least one of the people on the team has to have one of these skills. Probably throw in Diving there too, and maybe even Parachuting, depending on the plans UCAS has for them. For combat specialists there is more weapons training, obviously, hackers can pick up specializations for skills and program better programs, mages... actually I'm not sure what mages can do, they'll probaby have enough trouble keeping up as it is
Figure out the karma cost of the basic loadout, then figure out the karma cost for specialist loadouts. Give out the karma to people doing the training to raise their skills to the needed levels. Everything left over is theirs to deal with how they see fit. So if your rigger already has Demolitions 2 and your Demolitions training package includes Demolitions 4, then the rigger buys the skill up to 4 and blows the rest on Blades (Peeling Potatoes) 2.
Also, depending on how detailed you want the roleplaying to be, you can have training exercises and give out additional karma to people who do exceptionally well on those.
As for money, I would give them room and board and the basic allowance, and at the end of the training let them have access to a limited selection of military-grade gear. It wouldn't be top-of-the-line or even in great repair, and probably have some other restrictions on it, but toys are cool. Everyone loves toys.
Also, may I suggest finishing off the training by having them participate in a big wargame? You're no doubt already planning that, but.