If no third game to HGSS is ever made (not delving into that), then these are the changes I would make to the games so that they're the perfect Johto games:
- Make Kotone either resemble Kris a little more, or keep Kris in rather than replace her.
- Give Mt. Moon its BGM back (from what i've seen from clips, it now has the Ruins of Alph BGM).
- Have a 'RECALL' option for following Pokemon. It's clear that some people prefer travelling without the company of their Pokemon so it would've at least been nice if we had that option.
- Leaf cameo/battle. It would've been cool for Leaf to get some form of canonical existence in the games that gives her a status on par with Red who's a former/wandering Champion. For example, she could have been a Frontier Brain in what I think should've been Johto's own unique Battle Frontier. Which leads me onto my next point...
- A brand new Battle Frontier. I have yet to challenge anything on Platinum but the Battle Factory, but seeing that HG/SS has had Platinum's frontier more-or-less copy-pasted over makes the games feel a little... incomplete in my opinion.
- Completely refurbish the Gym Leader teams, particularly the Johto ones. It's depressing how this was one of the major gripes fans had with G/S/C, but the teams were largely kept the same. However, I have heard that the Gen IV mechanics and movesets make the battles far more challenging, so that I am looking forward to. :)
- Restore the Crystal encounter habitats (e.g. Hoppip on Route 29, Poliwag on Route 30/31, Phanpy on Route 46, Teddiursa in Dark Cave, Growlithe before the Violet Gym on Route 36).
Of course, having not played either game yet I haven't formulated a full opinion about them, but from the coverage on the internet that i've paid a lot of attention to, these are some of the things i'd like to fix in HG/SS.