OOH I KNOW! I KNOW!! :D
My Illogical Theory
Well, in the underground and in high-up places there are not many people around. Generally, in all the places you stated, there are not many people there, so it would be a great place to have an intimate final battle. 'Cos you know, if we decided to murder Ghetsis's Pokemon in the middle of Castelia City there would be people cheering and booing and throwing popcorn or roses or really annoying squeaky toys that would just take the full focus off of battling. I hope that wasn't a biased opinion since honestly I wouldn't want to have the final battle with Giovanni in the middle of Lumiose City with thousands of people watching. xD
And also, it must be cool to have a final battle where a legendary Pokemon once existed. I mean, in nearly all the places you stated a legendary Pokemon was/is/will be there. E.g. when you finally defeat Ghetsis in Black and White 2 you do it in Kyurem's presence. Or, Kyurem's previous presence. Wherever it was, Kyurem was there. And in RSE, you battle Archie/Maxie in the presence of Kyogre/Groudon. That must be pretty flippin' awesome.
Hope I helped. :)
