Alright you are right about the lvl cap thing, I should clarify what i meant about that more, what i really meant is that it is dumb to have a lvl cap that once you hit it, there is nothing left for the pokemon to gain or do. There are no new moves, no ways for it to improve, and it is now stuck with what ever abilities it has. I think once you hit 100 you should be able to chose what ever skills the pokemon was able to learn at any point and assign them, perhaps only be able to use 4 diff skills per battle that must be selected before hand, but let the pokemon have all the skills it learned, just switching them out.
As far as breeding goes, thats what i meant, it was a neat feature, but it took too long and you only could do one at a time, and there was always a small part of me that wished i could combine two diff pokemon to get a super awesome mix between them (but now i realize thats too hard to script/code) I like what they did in the versions with contests though, where the child pokemon gets its parents traits (high beauty that kind of thing) would be nice to see that improved upon.
Legendary pokemon where cool in a way because it gave you a goal to strive too, because they where so rare there was only 1 in the entire game. But they where wayyyy op (over powered) once you got them, and you pretty much focused on them entirely along with your one main pokemon after that, or at least me and my lil bro did.
I think another neat feature to add would be "ball creation" this could be done with an item creation script, where you have several parts that make up a pokeball, you know what instead of telling you this way, ill use examples.
A pokeball requires 4 parts to function:
Laser Core
Outer Shell
Memory Box
Power Source
So you have like 10-12 different of each part, and together they create new balls, each part adding its own stats/features to the ball.
A standard pokeball might be
poke core
red and white shell
poke memory
Battery a
Where as a custom ball might be made up of
BlueLaser Core - More effective against water and ice types (aditional 10% chance to capture water based pokemon)
Red and white shell - assigns ball image (a) to the item, and protects the ball from being broken (more advanced shells might allow for multiple usages of the ball if it fails once)
ultra memory - can capture pokemon of lvl xx or lower with 10% increased probability but loses 10% probability with pokemon lvl xx or higher.
Lithium Battery - balls with a lithium battery are capable of being retrieved as "dead balls" when they fail to capture a pokemon and then can be recharged at a recharging station
Maybe these arn't the best examples and some of the effects are impossible but the basic idea is there, and item creation where the item doesn't have to preexist as a recipe is possible (i think i have seen scipts for things like this) it would just create a recipie in that persons save file in the recipie book when that person creates that ball, so that it will log what they ended up with and what it took to make it.
This is also a way to add in more master balls, you can build one out of pieces you find called "master core" etc, that have a 1% chance of dropping off of select monsters.