Now I'm not one of those people who is deeply saddened about no Gen 3 remake (I would've liked one though seeing as Gen 3 came during a memorable time for me) but lets talk about the many similarities and nudges that Gen 5 had in its direction.
*Biggest one: The shoal shells and items. Unusable in Unova and was used mainly in Hoenn
*No soul dew when it was in Gen 4.
*The addition of Hidden abilities for almost every Pokemon is like how Gen 3 was the gen that introduced abilities
*Elite 4 battle theme has a motif that came from the Hoenn Elite 4.
1. They were also in FRLG/DPPt/HGSS... I don't understand why this means anything. All the items are coded into the games, regardless of whether they have use or not. (This allows trading.)
2. I don't understand what you implying. Soul dew was once again coded in every game. You could get it in HGSS and trade it to Platinum. You can also get it in BW2 and trade it to BW.
3. I don't understand why this would even be considered a hint. Because they expanded on a feature that resembles a feature from gen 3 it means they are planning a gen 3 remake? Maybe they were just expanding on a feature and allowing the metagame to evolve.
4. So many Pokemon songs are based off older ones. There are tons of youtube videos that compare different generation songs and show how some are extremely similar.
Hoenn gym leaders had new sprites created from the ground up for World tournament
So did...everything. The resolution is higher and requires new art. I don't see why this hints at anything either.. It's something they had to do to make it fit in the game. It wouldn't make any sense to have super pixelated art for a couple WT trainers and the rest of the game is higher resolution
Correlation does not imply causation http://en.wikipedia.org/wiki/Correlation_does_not_imply_causation
Look, I want a R/S/E remake. But some of these "hints" you guys are coming up with are huuuuge stretches and a bit silly. I'm not trying to be a dick but seriously... There's no need for them to "prepare" for the next game in the current game. Next gen is coming out and it's been rebuilt from the ground up, so why would introducing features or art now imply they are going to have a R/S/E remake? They would have to redo the art and code either way, so it's largely irrelevant.
Hints for R/S remake would be easter egg like things. For example, a character that mentions Hoenn in some way or implies something is happening there right now.