So, this is a really fun hack, brilliant idea. I always preferred double battles, and thus my favorite games are Colosseum and XD. There's just so much more strategy involved with doubles. There are a few notable bugs with the hack though and general issues I have with it. First the issues.
1, for some reason, Hyper Beam has no recharge turn? At first I thought you made it like gen 1 where there's no recharge turn if it KOs the opponent (which would be okay I suppose). I thought that because I first encountered Hyper Beam against Wattson; his Ampharos has Hyper Beam. Since every Hyper Beam was OHKOing my mons, I assumed that was the case. But then the second time I encountered Hyper Beam, a Claydol used by a trainer in the desert, I had Swampert out and it was able to tank a Hyper Beam. And... nope, there's no recharge turn. It used Hyper Beam again the next turn. You have a 150 power move (I'll assume the power wasn't changed) with nary a downside except a small chance to miss. I want to hope this is a bug. If this was intentional, I'm sorry, this is really stupid. Please fix this. It's broken as all hell, especially early on like Wattson where the only mons that could possibly tank a Hyper Beam are those that resist it, and even then they'll likely be 2 hit KO'd.
2, I don't have a problem with all the moves being updated to how they are in current generations. But if there's one move that should not have been updated to the way it works in current gens, it's Surf. Surf is like, required in gen 3 at all times because of all the water. And the game is entirely double battles. Thus you are essentially forced to have a move that can hit your ally, regardless of whether or not you want to build your team around dealing with that. Surf is not like Earthquake; with Earthquake it's easier to deal with because levitate and flying mons are commonly used, and if you don't use any (my current team doesn't have a levitate user or a flying type) you are not forced to use Earthquake. Surf though, you are, because it's an HM that is required everywhere lategame.
Those are my balance issues. Now for the bugs I noticed. First the major.
- when a Pokemon gets KO'd by Flame Burst, the game softlocks upon the adjacent Pokemon being hit.
- Route 111 was edited so the part of the desert where you find the TM for Sandstorm is connected to the path, so that once you get the Go Goggles, you don't need a rock smash user to proceed. Which is fantastic. You still get railroaded into beating Wattson first so you're able to use Rock Smash on the rocks, and need to do so until you get the Go Goggles. It's pretty clever. But there's a weird bug where randomly the map will load as it does in the vanilla game instead, where it isn't connected which requires you to use Rock Smash as you normally have to. I need to do more testing, but I think the map only loads 'correctly' (where the TM Sandstorm section is connected to the main path) when Mirage Tower is present...? I have not collected the fossil yet out of fear that is the case, but that's what it seems to be.
The rest I noticed are minor. The Hidden Power TM has a blank description. And a few cries are messed up. to name a few, Seedot's is weird, Combusken and Shiftry have a buzz at the end of their cries, and Blaziken and Nuzleaf have no cry at all.