First off, I'd like to say the custom opponent feature is AWESOME. I can easily add all the races I want, without messing around with xml sheets, and without worrying about any limit. That said, the list does get a bit cluttered after adding 10+ custom opponents.
That's why I'd propose introducing race categories. Every race would be in a category, and the race list would display one category at a time (selected from a drop-down box above the list). The random opponents option would only choose opponents from the current category. The user can add or remove categories, and there'd always be a 'standard' category with only the GalCiv races, and an 'all' category with all races.
This way, I can have a game with random Star Trek races, or pick Star Wars races from a list that isn't cluttered with standard GalCiv races and Babylon 5 races.