I'd like to answer the original question.
I've just some across this thread, and I've spent the last two days reading it. It has definitely sparked my interest in more places than one. I agree on most topics such as updating the music, expanding the storyline, and the like. I'd just like to put in my two cents about what might be cool in a remake for an actual game, and not just a fangame, like I am making.
-First of all, the GS ball was only available in Japan to receive Celebi. I think that it would be excellent if we could have something like a Wi-Fi Nintendo event to receve the GS ball, and the events would take place in the same way as normal, by giving the ball to Kurt, and then taking it to the shrine.
-It's not a particularly big issue, but it bothers me that the Viridian Forest is gone.
-The trading system. I know that no one likes to hear timeline theories, but...here's one anyway.
Maybe, you could use the time machine to get Pokemon from the past still. When you really think about it, all the games are actually behind in sequence from GSC. FR/LG are obviously behind, the games take place three years later in the same region. In FR/LG, you can connect to Hoenn via the Islands after you connect using the ruby and sapphire gems. All of the GBA games can “migrate” to Sinnoh, so it must be in the same time frame, right? Therefore, the games in Johto are about three years ahead of all the other games, which would enable the new game to use the time machine to connect to Sinnoh, without any conflicting time issues.
This theory is basically in case they want to include new items, TM'sm etc...one problem that I just realized...the apricorn balls that kurt makes. There is no sprite for those in the DPPt games, so this might actually be a good idea.
-Another solution to this problem, now that I think of it, would occur on the GTS. The GTS would appear as normal, but any Pokemon that have different items or anything else new would not be recognized in the DPPt games, and therefore would not appear on the GTS in those games. But they would appear on other games of the same type.
I hope this contribution makes sense...at least a little.
-PokeJosh