Yeah, though, I'll much rather take gbarunner2's speedier transitions because the accurate one feels extra punishing whenever you enter the wrong menu and have to go out when managing your pokémons on the terminal.
From an accuracy point of view, I noticed that gbarunner2 manages to run the handful of games that otherwise would freeze on agb_firm (obviously if you look the other way around more games will be playable on agb_firm, atm):
Army Men - Turf Wars
Justice League - Chronicles (U)
Rockman EXE 4.5 - Real Operation (J)
SpongeBob SquarePants and Friends Unite! (E)
Super Mario Advance 4 - Super Mario Bros. 3 (E)
Zero-Tours (J)
I'm not trying to say there's a competition, since they take different approaches to play gba roms. Also, I don't think Nintendo went in trying to make every gba game compatible with agb_firm - they probably focused on getting the few games they released to play as good as possible and maybe make sure that if they decided to release more games that they would play as well.
Between this and wireless linking capabilities, gbarunner2 will become my prefered way of playing gba on the ds family of systems. Heck, for me it's even better than slot-2 flashcards on the ds. I guess if you really want shaders, save states and cheats then maybe mgba/slot2 flashcards on 3ds is the better way to go. I don't think those things are within the scope nor even possible on gbarunner2 (?).