Kersenka

The EXP system is fine, the main problem is due to the wild Pokemon levels, they don't scale up properly as you progress the story. This makes levelling a lower level newly tamed Pokemon difficult, for example you could be level facing a level 50 gym leader but the highest level wild Pokemon you will face are about 30, this makes leveling a newly tamed Pokemon from level 30-50 tedious. If the wild Pokemon scaled per map to match the levels of the gym leaders it would be a faster levelling process.

I don't have vast knowledge when it comes to Pokemon, but from what I've seen so far and based on the Pokemon starting Pokemon choices in Johto and Kanto you pick from Water, Fire or Grass types. These seem to be the most known types, so for starters you could make NPC factions for these three types with quests and rewards related to that type. I don't see the need to make them warring factions nor do they have to be mutually exclusive, but if you felt you wanted to make them mutually exclusive you could do that, might make chat a bit more competitive. I think having factions based on types would be more fitting than random factions added with no real lore behind them especially since a lot of the Pokemon lore has trainers with favourite types, take gym leaders for example.