Well I can't say I didn't have fun while it was going. Thanks for running this CKY!

As for the system it seems to work well enough for its purposes. There are a few things I feel may be worth expanding on though you seem to have already picked up on them - pokemon moves, capture rates and all that.

Even if you don't end up doing a 'these are the specific moves each pokemon has and what they do' (which for the record I would personally be against) you may want to layout a quick overview of what each pokemon type can be reasonably expected to do. Kinda like 'Rock types are very hardy and can take a lot of physical punishment', 'Ground types can create tremors and burrow through dirt and rock at high speed' or 'Grass types can absorb energy from their opponents and many can produce spores and powders that can debilitate foes'. You know something to give people a general idea of there capacities without having to do an entire move list.

I'd certainly like to see this after your new ideas are implemented though.

I know this is late...
One thing I thought of today was in regards to the "list of moves" we kept bringing up.
What if, instead of a list of moves, you pick a type at the beginning of the pokemon creation (maybe even character creation). If an action relates to that type, you roll an additional die. Pokemon always start with a bonus associated with thei own type. But if they pick their type again, it's like an additional bonus. This would be in place of having a list of moves, it would be a result of training your pokemon. So maybe it would be better once your pokemon reaches a certain loyalty level (2 perhaps) they gain this as an ability as a result of their training.
Some examples, If you chose dark type, and you are fighting dirty, roll an additional die.
If you chose fairy and you are healing someone, roll an additional die.
If you chose water and you are watering something roll an additional die etc.