So since the start of pokemon games the rpg element has always been on the pokemon aspect and not the trainer aspect. Reading through the ideas for the game written by the development team I saw they were doing something about more experienced trainers are able to catch pokemon easier and what not.

How about allowing the trainer to gain experience and levels when you win battles and defeat wild pokemon. When the trainer levels up you can allocate stats into the 6 base stats the more in a given stat the higher your pokemon's stats will be of that given stat. So say your trainer starts at level 1 with 5 stat points you can put them all into one stat say speed and all your pokemon would get +6 to their speed stat or it could work like EVs in that every 4 points your pokemon get 1 point in the specified stat.

Also trainer types could give certain advantages and disadvantages adding an entire new depth to pokemon meta-game. For instance when your trainer reaches a certain level you can choose your main type and possibly at a higher level you can choose a secondary type. Each type would have it's own pros and cons.

Just some examples of what they could be
Primary:
Fire - when your pokemon are struck by attacks it causes the attacking pokemon to become afflicted with burn status.
Or fire attacks used by your pokemon deal 50% more damage
Negative could be all your pokemon have 2x weakness to water, rock, or ground.

Water - When any of your pokemon enter the field they summon a down pour.
or water attacked used by your pokemon deal 50% more damage.
Negative all your pokemon have a 2x weakness to electricity, or grass.

etc etc

There can be really cool effects and the secondary effects could be less powerful type effects.

A cool one for rock would be you start the match with stealth rock on the field.
Flying could be all your pokemon have a 50% less chance to be heat with ground attacks

Tell me what you think any all are suggestions/criticism is appreciated = )