On the DSi, you can use both GBARunner2 and GBARunner3 at the same time, and they have some differences in compatibility.
I’m playing a ROM hack of Pokemon Emerald on GBArunner2, and it’s running fine.
TWiLightMenu++ uses GBARunner2 by default...
Development on GBARunner3 is paused, as the developer is currently working on DSpico stuff. It may take a while before they get back to working on GBARunner3 again.