Two questions:
If I have version 2.9 but want to try the Repo route, do I need to uninstall my current setup?
it is the cleanest way, first remove gamestarter addon, then install retroarch, emulationstation, AEL... by the moment this change needs some manually folders removal, that is not yet explained (just removing /storage/.config/emulationstation and /storage/.config/retroach).
So if the addon is working ok for you and you don't want to spend some time to get it working you better stuck on addon, until addon gets outdated...
2nd question: Can I delete the various consoles in the list in the AEL if I don't have ROMS for it (and never will) ? I just want NES and SNES to come up for example.
of course, it is just a default list, you can add or remove the systems you want.