The best solution would be huge condensing of Commanders and revamping them into a Doctrine system, and then stop selling them full stop.
But Relic/SEGA/Whatever asshole's in charge is a money hungry prick so that will never happen. Let's forget that, then.
Failing that, and being stuck with this god awful commander system, simply make sure the three commanders you pick combine into a tree structure as opposed to "I have three but I can only pick one", you pick your three prior to the game and work with everything they have.
It might even be a bit more enjoyable than the old Doctrine system, allowing for much more variety and mix/match, while preventing the sad souls who paid for that garbage from crying.
Mixing and matching would probably present 439257893487593825 more balance issues. The Idea of having those set skills per commander is to push a certain strat per commander. Relic can control each commander separately that way.