Performance is important to me so I probably won't use those options, I'll give my 2 cents regardless.
How important is it to you for the startup screen to fade into the game? Is it worth the performance sacrifice to you while playing the game?
Not at all, but I usually go for the less flashy/faster transitions just for performance.
How important is it to you to use bezels? Are they worth the performance sacrifice to you?
Most emulators that I use bezels with already have the option so I don't really care for external programs.
What features are you most looking for with startup screens?
Just a black screen or the game wallpaper/logo with a loading text in somewhere, the bare minimum so it doesn't feel like bigbox might activate randomly while I play.
What features are you most looking for with pause screens?
Not to big on external pause screens but if I had one... probably reading manuals and quitting the game.