Well, I'm pretty much out of room for lobby options, period. I know there is future stuff I'm going to need, plus there is this sort of issue with splitting out these various other functions, etc, so that they can be more specific (like the enemy waves) or used in conjunction with one another. The only way I can think to do this is to make multiple tabbed pages of advanced options, which initially I had wanted to avoid just so that people wouldn't have to stare at so much complexity there. But, now that it's unavoidable, I think I'm going to redo that entire section of the lobby so that it is a bit more flexible and also has more room for expansion, since that's going to be needed. These are good points that you've raised, I've added that to my list for part of that process. Even at the original release of the game, there just were not nearly so many options for the lobby, so it wasn't an issue until all the new things have been continuously added!
The easiest way to handle the whole complexity problem would be like how lots of game handle graphics options; one low/medium/high/custom box that just fiddles other options. You have say for the ships, a simple/average/complex/custom combo box on the first page which just fiddles with tick boxes on another tab that does the actual configuring. If the user changes one of the tick boxes on the "advanced ships configuration" tab, it sets the main combo to "custom" to notify the user that they've done something non-standard.
You could handle AI waves and the like in a similar way; none/few/normal/brutal/custom (which is configured on the advanced page). And so on and so following and so forth.
Gives you the best of both worlds a nice quick/simple setting for new users or the lazy, and something for people who have way too much time to fiddle with.