The idea is that the permanent bonuses would be a lot more expensive. Quartermaster, Procurement Expert, etc. Each would cost 1000+ XP and you would not expect to get them all anytime in the near future. It would give a slower progression than currently. You could have levels of each one, say three tiers of Quartermaster giving +1 or +2 dudes each.
You COULD split XP into permanent XP for leveling up the commander, and Credits or whatever that could be spent. First of all, this helps "retain" XP progress and seperates it from spendable credits. Certain upgrades would only be unlocked at a certain Commander level. In particular the permanent upgrades above. Also, any particularly advanced weapons tech trees such as Gauss Gun, Death Ray, MegaPlasma. Certain ships could be unlocked at medium commander levels such as the Visio, Harvester, TurboSpeed one, etc (and get rid of them out of the researchables and replace with a plain +10% extra level). Those ships would be cool to play with early game.
I probably would not provide much in the way of passive bonuses to the commander level though. Maybe one small bonus per rank up perhaps. I prefer the unlockable permanent-upgrade approach a bit more. Gobbles more XP.
Keep in mind that there are only 4 weapons tech trees right now. They are not very easy to mix and match, so 4 major paths to victory more or less. You can try to splash to get gatling PDs for example but in general it is not worthwhile.
If you added another 20 or so researchable items, especially if they are not necessarily locked one-behind-the-other or of different sizes, then there are exponentially more combinations to try out.
Especially as I tried to create items that were more specialized, moreso than general purpose.
