4th Gen and onwards had a lot of very mechanical QoL changes with things like the Physical/Special split, the new EXP curves and boosts in Black and White, the party wide Exp Share, reusable TMs, so on and so forth. While most hacks pick and choose stuff like this to include, you're going to have a hard time finding major hacks that don't have the Physical/Special Split.
Additionally, a lot of hacks that put in older regions tend to make rather sweeping changes elsewhere, but the work for the extra regions has certainly been done. Most are attached to Fire Red (or RPGMaker) for ease of development from what I've seen.
The "Complete Hoenn Dex" you linked is probably your best bet for what you're looking for. It has indoor running shoes, day/night, and a lot of other little changes to ease some of those GBA frustrations. Beyond that, have you tried or thought about trying Alpha Sapphire or Omega Ruby on 3DS? Obviously it's not quite what you asked for, but most of the completion and QoL issues from the original games are complete non-issues in the remakes. The new EXP Share will overlevel you considerably though, so you may want to think about leaving it off until you need it to enjoy the original level curve.
