I was trying to think up ways to make the regeneration and carapace combination less desirable, and thus perhaps restore to the player full control over which upgrades they would like. Then an idea came to me, what if some upgrades, or all of them (though that may be difficult), directly magnified the benefit of other upgrades? Or even changed how they function all together?
For example, carapace and regeneration. Perhaps when taken together, regeneration could only heal armour, but at an increased rate and works while under fire. It increases your combat survivability but still requires you to retreat to a gorge/base for healing.
I'm not sure what could be included for other combinations, (anything else I came up with seemed useless and contrived), but I think the above could work pretty well. And I'm aware that this hasn't a hope in hell of being in the game before 1.0. :)
Would also need to address celerity and adrenaline for the Lerk too though, if anyone has any ideas. :) Though perhaps that combination can be forgiven, since without carapace they die to one well-placed shotgun blast.