[@BCTheEntity]

I had thought about players having more then one partner. I was going to give them two more down the road in the RPG to help with the battles since I'm going with the first season of Digimon's consent were the Dark one controls other Pokemon with some kind of device. now that you bring it up I might edit the CS because I'm thinking each player could get four Pokemon partners. three non legionaries and one legendary. 

For the TM's and HM's. I actually was going to use them as digital codes scattered around the world that can be scanned with the players phones. also, since we all know once a Pokemon uses a TM or HM they lose the attack they replace with the TM or HM. I was going to have a sort of storage system for attacks were the trainer can still keep all the attacks their partner knows so they can simply swap out attacks without losing any attacks.

as for Fly, surf and abilities like that. I'll allow players to ride on their Pokemon, but only if the Pokemon can carry their trainers. also, Pokemon that can already fly can carry their trainers, but only for a short period of time. if they wish to go longer, they'll need Fly for that. 

TM's and HMs' will be scattered all over the world, but for many of the parts in the RPG. some TM's will be necessary, but NPCs will help in finding aid HM's or TM's.  

I hope this helps and I'm not too confusing on my logic.