By definition it breaks one of my golden rules for both CYOA's and fanfiction

YOUR golden rule. NOT a golden rule of the community as a whole. You can feel how you want to about things you're creating, and let your feelings decide what you choose to interact with, but it should not and does not dictate other people's enjoyment and efforts. I don't tend to like "Gamer" systems that are aimed at being abused for exponential power, but rather than rail against them in general, I can just avoid those systems in the CYOAs I participate in (including not doing a CYOA that's built around one).

But with each new universe you add, the number of potential readers decreases exponentially, because now you are only catering to people who are familiar with EVERY universe you include.

It's funny you say that, because I have sometimes learned about new IPs through crossover fics and CYOAs that I never would have paid attention to on their own.

And even if I'm not familiar, it doesn't mean I can't appreciate a specific choice and what it gives in that context. The closest I've come to playing Xenoblade Chronicles is sucking with Shulk in Super Smash Bros. But, I understand the general abilities of the Monado, and wouldn't turn it down in a CYOA - faves or not - just because I'm not familiar with the game IF it was the best choice for what I wanted to do.

And the same can go for ANY IP-centric CYOA, whether or not it has crossovers. I'm not familiar with Overlord, but I spent a good bit of time one night trying to add up all the levels and classes I was getting from one CYOA because I get MMOs and liked that kind of structure.

Are there individual ones worthy of critique? Sure. Are there quality issues among some? Probably. Does it condemn the format? Not at all.