Madagascar could have been colonized from Southern India instead of Borneo (which despite being the OTL event is the more unlikely one and runs against dominant winds and currents in the Indian Ocean).
Yeah, couldn't the Malagasy been spawned from a different Indonesian group, or as you said, the Indians. Which that might be interesting in the long run, since if it were settled around the same time as OTL, that would be after Buddhism and Hinduism influenced South India. Tamil nationalists would probably love it and promote crank theories about it.
Also, don't forget the islands surrounding Madagascar. The Seychelles, Reunion, Mauritius, etc. all could've been settled by various groups that would've created a unique ethnic group. Really, OTL, they could've had been settled by the Malagasy and produced a separate yet related group (more separate than the Malagasy subgroups). Though if they didn't have much contact with the outside world, epidemics would decimate them and they'd end up merged into the mixed population imported by European colonialists. Also, the Arabs might raid the islands for slaves, since the Arabs did know about those islands. Incidentally, an Arab group living on those islands would be another example of a potential ethnic group.
I've been a huge fan of more Polynesian groups--the Juan Fernandez Islands, Galapagos, and Cocos Island (in Costa Rica) all could've have unique Polynesian groups, likely most closely related to the Rapa Nui linguistically. The sheer size of Galapagos could make it like a second Hawaii, albeit heavily dependent on rainwater from the rainier parts of the islands which would keep the population down (and influence culture/political development in very interesting ways, no doubt).
I could go on with this--if you have an uninhabited remote land, once you get far enough back in history, any human settlement of that land will create a separate and unique ethnic group. There's so many islands which were uninhabited until Europeans colonised them which could fit this role.