I was personally enjoying Pokemon Shiny Gold, a gold remake hacked from Pokemon Fire Red that was around before the REAL second generation remakes and it even contained third generation pokemon. I wanted to start a new file on it but my VBA controls don't seem to be working so I am waiting for a response on how to solve the problem on Coolroms.
I was also at one time enjoying one called Pokemon Generations which is a red hack that rearranged all of the scenery and gave the gym leaders their canon teams from the anime. Brock had vulpix in place of geodude for example(or maybe he had all three I can't remember for sure). You play as the G/S/C sprite, your starter choices are Mew, Dratini or Eevee and your rival is Ash who wants to relive his adventure after finishing the league.
I never managed to get far though, I originally discovered it via a gaming website where you could play and save the games directly onto your account but the stupid thing never worked. My place would never save. It pissed me off I really liked the team I made and I ditched the site after a couple of this occurrence.
But then, not long ago I found a downloadable version so yay.
I have not played my VBA for a while, I may get back into that game as well.
There is this one called Pokemon Frost, a Ruby hack that is not that well done but the rival meeting was awesome. I don't know how it works if you are May since I was Brendon(I always am, I hate May, she's ugly and annoying) but when you meet May she's looking at porn and says when she heard there was a new kid in town she hoped she could screw you or something I forget exactly(Instead of hoping you could be friends). Then asks you not to rat her porn out to Birch lol. I found that so funny, but it was the only good part of the game.