You can lean into it, like Disgaea, which just embraces the brokenness and writes them into its mechanics. You can just sort of write a standard game, but then, in the end, the solution to all problems is grinding. You can scale the challenges with the level, but then, what's the point of leveling? In fact all you're doing is running the risk of showing just how busted the mechanic is when you have a hard time matching the levels correctly because of the exponential power gains; see Oblivion, for instance. And even after such a mismatch, the solution to all problems is still grinding.
Obviously many fine games have used this and I still play some to this day, so I'm not saying it's never ever fun. I'm just saying, the ways in which it's kinda broken seem fundamental and there seems to be only so much you can do with them. Were I designing a game today, rather than treating it as a default as so many designers still seem to, I'd want to take a careful look at the disadvantages and be sure I'm comfortable with them before proceeding. And as a gamer I do have to say more and more I'm starting to mark a game using level-based mechanics down a point when I'm figuring out what to play.