Just played through this. So much fun! If I could add only one thing, it would be nature mints or some other way to change the nature of already captured mons. I found a wonderful set of AR codes to change the natures of all newly generated trainer pokemon. I implemented it about halfway through my playthrough after getting a -spatk Suicune. Unfortunately, it is very tedious.
I guess if I could see anything else, I'd want Protect and Helping Hand available from as early as Phenac. At least by Agate.
Also, for some reason, I don't think thick fat properly triggered on fire type attacks aimed at tropius?