In my experience as a player, something like regular store items like Revives or Hyper Potions even can be nice, but it could get somewhat old fast, and plus, what's the point of buying that kinda stuff then if you have the items already, or tons of cash? Special (apricorn e.g.) balls can be nice too, though, if you already have one route done, it would just allow you the ability to keep going for the reward of more balls which is... not conducive to exciting a player in the long run, unless something bigger is teased somehow.
Then, if single-use items are not considered, the best thing would be consumables. Depending on how you want to do your game, TM's might be a way to go, especially some of the more wacky ones like Ally Switch, Quash, Infestation even. Though, I wouldn't put anything really good, since it would discourage multiple playthroughs from someone, say, playing the game for a different team + battle experience that would therefore benefit from lots of TM coverage yet would not want to re-collect every available species on a route. Perhaps some other kind of collectible would be nice in their place, then, such as perhaps legendary items (Silvally Memories, Arceus plates, maybe?), the type boosters (SilverPowder, TwistedSpoon, Black Belt, etc) or something else you've thought of uniquely for your fan-game, such as exclusive boosting hold items (Thick Club, Light Ball, e.g.), maybe for the most rare mons on the route? These are just things I could think of that would make someone want to collect all the species in a route beyond just the benefits inherent with, well, having all the mons from the route. Hopefully this little ramble helped, even just a bit?