Maybe Battle facilities will be spread out throughout Kanto and Johto, that could explain the new buildings next to the radio tower and the national park. It could mean that the battle tower has kept its place from crystal, as it does appear to have done from the zoomed in image somewhere in the PC. The new area west of Cianwood could be a new facility where battles take place on different terrain (highly unlikely and probably going to be a safari zone or pal park) the other facilities could be spread out in Kanto, maybe 2 or 3 of them? This is just an idea but it would be interesting as each facility would have its own personality.
In my opinion it would be a shame for "The great Sea Basin Pokemon" to not have to be dived for as that is the thing that i remember it for and what makes it unique. I think either HM or TM Dive should be reintroduced in order to catch it or the quest should involve some sort of submarine. (a bit extravagant, i know)