That's what I think. Even though gen 5 can be played on old DS/DS Lite, recommended platform is DSi because of Xtransceiver. Also, gen 5 has no option to use dual-slot (dongle) mode because DSi has no GBA slot. It makes gen 5 looking even more to be made especially for DSi. If we treat gen 5 as DSi generation, R/S remakes make sense to be made in gen 5.
One, it's not necessary to go underwater to get to the final gym, you have an option of taking the tunnel or going through the route. But this could be connected to the final town/gym type theory.
If you played Black, Iris wasn't a gym leader so the relevance of events can't really be used. Hence why I didn't state that as Iris was already hinted at becoming stronger in BW. Still I see your point.
Music changing can't really be a hint as in every game that has a major change happening the music changes. It goes with the mood.
Actually, crisis and temporary music change caused by power of legendary Pokemon is something featured only in R/S/E and B2/W2. I don't mean short music changes at the moment while Pokemon is appearing. I mean Drought/Flood music from R/S/E and frozen Opelucid music from B2/W2.
You're right that those things from B2/W2 aren't exactly the same like in R/S/E, but that's actually good thing because they resemble R/S/E but have their own style at the same time. Also, Hidden Hollows scream Secret Bases. I really think we should except R/S remakes in gen 5. Hoenn is being hinted in B/W/B2/W2 like Johto was being hinted in D/P/Pt.