While I haven't played altogether many hacks, this one is my absolute favorite by far. It's the only hack I've come across that is heavily based around what appears to be developing into a deep and very gripping story. I loved the cliffhanger even though it was spoiled because I read too much of this thread. There were some parts of it that I thought were a little forced like the fact that the main character is suddenly a robot and the deal with timeless grove, but I won't be too critical because I know you've already completed the story. I would just recommend maybe lengthening the opening a little. I don't know how intensive that would be but I don't think it would be too hard to add a few more lines of dialogue and maybe make the run through the base just a little longer. It just felt really fast with the 'leg-enhancements'.
As far as game mechanics go, there was only one thing that I felt was somewhat annoying and that was how hard it was to find the second exit to the Silvertone Sewers with so many doors. There were also a lot of trainer battles down there, perhaps a few too many.
The only other thing I might suggest is perhaps modifying the starters a little more. To be honest, with the exception of Ralts, I found them to be rather off-putting. Changing the stats and some of the moves was nice, but I think you might even be able to take it farther. For example, you could give Ralts moves like Shadow Ball, Shock Wave, Disable, Psywave, Confuse Ray, Recover, or Mist Ball. You could give Seedot/Nuzleaf moves like Quick Attack, Mach Punch, Detect, Sleep Powder, Stun Spore, Spore or Beat Up. Machop only has normal and fighting type moves so you could try things like Rock Tomb, Fire Punch, Ice Punch, Thunderpunch, Earthquake, or Outrage. I also thought Pound would be more appropriate than Tackle for Ralts but whatever.
I like coming up with interesting and surprising movesets for pokemon, but those are really just ideas that I thought I might share if you wanted to steal some of them or use them to help think of some movesets of your own, or not. I don't want to get in the way of whatever direction you're taking this hack.