Ok, per your request, here's what I've put together with a limited focus on just a few skills.
Proposal:
Option 1:
Command XP
Characters earn Command XP = to the number of unit missions (not solo) played in each contract they take part in. Command XP can only be spent to increase Admin, Bureaucracy and Negotiation.
Contract / Command XP / Lance Start
Pokey /3 / Mudd (Dancer), Breisacher (Crusher)
Themyscira / 5 / Brightsword (Bright), Wilhelm (Reaper)
Running Horse / 6 / Hartman (Freya), Kronwall (Skaraborg)
Slammer / 3 / Atayde (Midnight)
Henhouse / 5 / Cherikov (Wolverine)
Kestrel / 5 / Malthus (Phoenix)
Sudeten / 3 / Moon (Ice)
Liber / 3 / Hitzig (Dragon)
Justice / 2
Tukayyid / 3
Angel / TBD / Roskakoriinnen (Devil)
38 XP starting at Pokey
Starting Values
Breisacher (A: 0, B: 1, CS: 1, N: 1) [Pokey]
Mudd (A: 0, B: 4, CS: 1, N: 1) [Pokey]
Wilhelm (A: 1, B: Nil, CS: 2, N: 2) [Themyscira]
Brightsword (A: Nil, B: Nil, CS: 2, N: Nil) [Themyscira]
Hartman (A: Nil, B: 2, CS: 4, N: 2) [Running Horse]
Kronwall (A: 1, B: 2, CS: 2, N: 0 ) NOTE: No PC creation thread I could find [Running Horse]
Atayde (A: 2, B: 2, CS: 3, N: 4) [Slammer]
Cerikov (A: 0, B: 0, CS: 2, N: 2) [Henhouse]
Malthus (A: 1, B: 1, CS: 3, N: 1) [Kestrel]
Moon (A: 1, B: 0, CS: 3, N: 2) [Sudaten]
Hitzig (A: 5, B: 3, CS: 3, N: 5) [Liber]
Roskakoriinnen (A: Nil, B: Nil, CS: 2, N: Nil) [Angel]
Notes
While several entries are listed at 0 in Google Sheets, they're actually Nil
Mudd bought Admin to 1 (7 XP)
Atayde spent 21 XP to go from Admin 2 to 3.
Under the proposal above, here's how much command XP people would get:
Mudd: 38
Breisacher: 38
Brightsword: 35
Wilhelm: 35
Hartman: 30
Kronwall: 30
Atayde: 24
Cherikov: 21
Malthus: 16
Moon: 11
Hitzig: 8
Roskakoriinnen: 0
If Mudd focused all of his Command XP on Admin, he'd be +2 up from +0 and able to make +3 after this contract. That would leave his Bureaucracy and Negotiation untouched, and he's been around since the campaign's beginning. Brightsword's 35 would mean all 3 Command skills could be at +0 with 1 closing on +1 having only missed Pokey.
Career XP
I would suggest an additional XP award following the same criteria as Command XP. In this case, both Mudd and Breisacher who have completed 10 contracts and been active as Mercenaries since May of 3044 (almost 9 years gametime) would go from CS: 1 to CS: 3 at a cost of 35 XP, so with 3 left over. To reach +4 assuming 3.8 XP on average and needing another 25, it would be 7 more contracts.
Rationale
The goal is to keep things simple rather than add a bunch of extra book keeping. The advantage to the above is that you can always calculate it if there's ever any question and you have the baseline for all PCs, so it can be corrected as needed. Through the entire campaign other than myself and maybe Steve, no one has spent on any of the 4 skills mentioned. Honestly, I'd be almost willing to bet that virtually no one has spent on any skills outside of P/G and maybe Scrounge since generating their character. So while I agree the goal is to avoid making letting everyone get elite skills unless they've been around forever and have earned gobs of XP, the way the campaign is structured I don't see that happening. With the frequency that other skill rolls get used, I don't think anyone would consider it a difficult choice to select Admin, Bureaucracy, Career: Soldier, First Aid, Leadership, Negotiation or Small Arms against Piloting, Gunnery, Scrounge or an SPA. Tactics might depend on whether a PC is up the chain of command and even then I think it loses. For most PCs Strategy only comes into play when there is a reinforcement lance to select. And to be fair, I don't think I've ever heard anyone say they would have brought in X lance except they'll arrive too late. There's also a certain homogeneity with every PC lance except Devil having either a 3 or 4 strategy. In general, this all works fine it just means PCs are essentially only changing a few skills and SPAs barring aging or catastrophic events. The Apocalyse Rising Campaign made greater use of the broader skill set and so it made sense that people would invest more in other areas. Different campaigns, different flavors.
I don't think the numbers listed above break anything, but with the request to essentially make people make choices, Option 2 below puts more skin in the game.
Option 2:
As option 1 above but with the following change: Command and Career XP can only cover as much XP as your current level. So assuming you have enough C/C XP available, here are the costs:
Level 0 (from Nil): Level Nil is 0 XP, Level 0 is 10 XP, C/C XP max: 0, Real XP cost: 10
Level 1 (from Level 0): Level 0 is 10 XP, Level 1 is 7 XP, so if you have the C/C XP, can pay to get to Level 1 with C/C XP entirely
Level 2 (from Level 1): Level 1 is 7 XP, Level 2 is 14 XP, C/C XP max: 7, Real XP cost: 7
Level 3 (from Level 2): Level 2 is 14 XP, Level 3 is 21 XP, C/C XP max: 14, Real XP cost: 7
etc.
All this assumes you have the C/C XP available, it costs you 10 Real XP to get to level 0, but level 1 will effectively be free and then 7 Real XP for each bonus after assuming you have the C/C XP available.
This means you get a benefit, but you still have to invest something.
In terms of what it would mean to Atayde, for simplicity sake I would leave his starting point as it is and not look to get XP back on Admin 3, just have the options available moving forward.