The only real hints I could classify as actual points that relate to Ruby & Sapphire are the fact that they re-introduced Dive, the Shoal Salt & Shoal Shell and some music similarities, other than that references to Hoenn from characters in the game couldn't really be defined as hints.
I agree, only those things could be potential hints, but even those have other purposes in the games. Though Dive is an HM again, remember that De Fog was one in D/P/Pt, while it was replaced for HG/SS. So the HMs don't have to be the same for every game in a generation. Also, many people are speculating that there could potentially be more use for Dive in B2/W2 going by designs of the new areas and the PCs' outfits appearing to have wetsuits under their clothes. Personally, I'm not sure what to think of that just yet.
Shoal Salt and Shoal Shell are more interesting to me, but according to the item description, there's someone in B/W that will give you a lot of money for them. This could have just been an alternate way to make some big bucks, while reusing an older item and harken back to Hoenn, but if anyone wanted to claim they found a hint, these items would be best for it.
R/S remakes most likely are going to be in 5 gen, there are MANY hints to suggest it. By ending gen 5 soon I meant two main games in this year (B2/W2 and remakes) and 6 gen game for 3DS in 2013. This would make gen 5 shorter than gens 3 and 4.
Most of the hints you've suggested can be disputed though. You said the music was a hint, however, the Team Rocket challenge theme was completely redone for B/W, and though I can't remember who exactly has it (Battle Subway guy maybe?) but someone in B/W has the Final Battle theme from RBY's Champion battle against Blue. Not to mention Cynthia herself being in the game with her theme. The only music I heard in B/W that reminded me of another game were the themes for the Tao Dragons, which part of sounds like one of the Routes from RBY.
You also have to remember that the anime is supposed to move faster than the previous generation. According to what I read, Ash will challenge for his 7th badge next month. I've seen several people suggest that the 5th gen saga could be over this year, since there seems to be no sign of anything filler in the works. But anyway, I highly doubt that we'll see another main series game this year. Releasing games too close together can potentially affect sales. And look at what holding on to the Wii so long is doing to Nintendo, they're losing money. Everyone has a Wii now, so no one is buying them. They need to start pushing the new technology right away. They need to give Pokemon fans a reason to buy a 3DS. The AR Searcher is a step in that direction, but only a full main series game will convince the majority to buy one.
Btw, this might be interesting:
We know that Kyushu = Hoenn in Pokemon world. Does that mean Shizui is from Hoenn? If so, we might meet him again in R/S remakes while he would be visiting his home region again.
I don't really look into the Japanese side of the games that often (from the US), but that is an interesting find. He may have moved from Hoenn to start some kind of business in Unova in addition to becoming a Gym Leader. His design looks as if he might be a sort of fisherman to me. Though, this could just be a tribute to Hoenn and not a hint. (just because it's Hoenn related don't necessarily mean we're going back to Hoenn.) Like I said, many other points of the game were related to Sinnoh as well, such as obtaining the orbs for the Sinnoh dragons and Cynthia. The Team Rocket appears theme was strange because the only purpose it had was just to hear it. And while many more people did mention Hoenn in these games, other regions were mentioned just as often. I personally did not see the number of people mentioning Hoenn outnumber the people mentioning other regions.
I'd like to know if all the characters in Hoenn speak with the Kyushu dialect as well. If they do, there's a chance he could be originally from Hoenn.
It's very likely R/S remakes will be part of 5 gen, meaning they will be next main games after B2/W2. B/W and B2/W2 are referring to R/S/E in the same way like D/P/Pt were referring to G/S/C. There were doubts about G/S remakes being done in 4 gen, just like there are now doubts about R/S remakes being done in 5 gen.
I'd say that most of Hoenn Pokemon sprites got completely redrawn in 5 gen to be used in R/S remakes. I think new addition in remakes will be new animations for Hoenn sprites, just like they added new animations for Unova sprites in B2/W2.
I think the doubts about HG/SS were probably justified. It's not often that you hear of a company remaking old games on a regular basis. However, since they DID remake G/S/C, now everyone thinks it will be something that happens every generation. But here's the thing: now there will be a need to remake FR/LG because they are incompatible just like R/S/E. Should Game Freak remake those too? The more they remake old games, the more problems they're gonna have. Then what about next gen, would we see Sinnoh remakes? And though we are still in Gen 5 at the moment, Gen 7 would call for remakes of these games! The "remake cycle" needs to change, and I think the best way to do that is to wait on R/S/E remakes for now. Every generation doesn't need a remake. Plus, I think this generation is low on spinoff titles and console games. The next Battle Revolution-like game would keep us happy until gen six if it were to come out sometime maybe at the beginning of the year or so.
As for the sprites, if you look at Groudon and Rayquaza's sprites from Gen 4, you'll see why that changed them. They appeared to be in some sort of victory type pose, but the new animations give them a natural animated appearance that I don't think could have worked with their previous sprites. Also, Hoenn Pokemon weren't the only ones to get new sprites for their animations (one of my personal favorites Arcanine was upgraded too) so go by those alone. Even some Sinnoh Pokemon were updated despite having the most recent graphics.
