Fellow game dev here,
Just chiming in to say how fantastic this game (really, it's unfair to diminish it as a "hack" at this point) was coded, edited, polished, and well, everything that everyone else here has mentioned already. It's amazing to see somehow who shares the same passion for the series as myself turn that into a tangible game which goes above and beyond at recreating the authentic Pokemon experience. At the risk of sounding redundant--to say this hack is exceptional and unique is an understatement, so congrats on finishing the main story!
Onto my specific likes and dislikes:
* Pokemon selection is fantastic and balanced. A few fan favorites were missing early on such as Riolu, Togepi, Zorua, Trapinch, Axew, and maybe others that I can't think of at the moment. Overall though, the logistic reasons for Pokemon selection was sensible and fitting, and had an uncanny resemblance to how GF organizes/structures their Pokemon selections. I could be more specific but I think you get the idea.
* Mega Evolution implementation blew me away. Who would've thought GBA hacks would receive these kinds of features around the time Glazed and Light Platinum came out? The cleanness and polish of the function defines this game as the next generation of Pokemon hacks. As an aside, Mega Altaria with Dragon Dance, Return, and Earthquake sweeps quite literally everything not named Skarmory once you get it. I only wish the 3 Hoenn starters and their Megas were obtainable, especially considering they seem to be some of the most popular Megas out there.
* Story is very good, although there were a few moments where I could tell the limitations of the hacking engines were holding back the narrative. It's not easy to write a thorough story anyways using only the 2D utilities of a GBA rom, so this isn't really a gripe as much as it is an observation. I did really like the circular narrative and the worldbuilding was very nice, although a little force-fed at times. There was also a lot of off-screen action; like how we don't see the 3 Regis even though we learn that the Elder Knights capture them multiple times. Again--just observations. Nothing needs to be fixed here, really.
* Loved the QoL features. These are so underrated in ROM hacks that if some hacks don't include certain features/fixes I might just stop playing altogether. IV grades are something that everyone should implement, and god help me if I don't receive my Premier Ball after buying ten Poke Balls.
* Mapping was good, although not very consistent. I figured out quickly where hidden grottoes were because I realized they only popped up when certain tilesets were used. If possible, some hidden grotto tiles for the jungle tileset or the snowy forest tileset could be very nice (perhaps even underwater caves or rabbit holes could be utilized). Personally I think all of the Hoenn assets should be replaced with the Sinnoh tree tiles, but that's an arduous task I would never push on a fellow dev--mapping is already hell as is.
* This game would be very well-rounded out if it had an original soundtrack, but that's not an easy thing to ask for. I guess it was just a bit offsetting to hear the museum theme in the hometown and then all the Hoenn tracks that I've heard probably over 10,000 times pop up in different towns and routes. Just a personal gripe, and by all means not a big one. For what it's worth, I loved the original tunes that did play here and there, such as the Elder Knights' theme.
There's so much more I could type here but I think it's more than evident that others have left enough feedback to keep you busy for years. So all I'll say is congrats again on completing the main story and nothing but the best of luck in finishing the hack! I haven't had this much fun playing a rom hack since Vega, and it's even more exciting for me to know that you're still chugging away making this game the best it can possibly be. Cheers!