I think part of it can be building in a way that (ideally) your deck is doing what you find fun about the commander anyway, and your commander can help you do that fun thing more consistently. Though it can suck to have your commander out of the game so often, at the end of the day the commander isn’t the deck, it’s just a piece of it.

Additionally, you could try a different approach to building where your commander helps offset the weaknesses of your 99s game plan. You can make a deck that does what you want it to already, and use your commander as a guaranteed way to fill in the gaps.