i know it isnt negotiable but this is how i see breeding.. if at any point in the game breeding is released.. pokemon should only be allowed to be bred one time, not with a ditto unless it is another ditto, and pokemon hatched from an egg cannot be used for breeding, ivs would only slightly go up if at all and cannot go above lets say 10-20(randomly lower number if some ivs are already higher than 20), natures should be random, and breeding should only produce a shiny at a very small chance if both parents are shiny. and if it is still considered a potential game breaker.. make one or both of the pokemon "run away" after breeding(breeder can "lose track of pokemon" and its a random risk).
this would allow for a few things to happen, 1 it could be made challenging to obtain pokemon that can only be hatched, 2 the ability to give event pokemon out as eggs or even marked as having bred before/unable to breed at all, 3 giant gold sink for those that would want to obtain a shiny pokemon in this way with halfway decent ivs(i only fear for the shinies safety after being... :Frown: ), 4 it would only produce a well rounded pokemon that isnt a monster.
enough on that though since it would actually require a lot of work..
on to flying.. if flying itself is the gold sink then it wont be worth using it often. you would have to make the gold sink come soon after flying or in another form such as a license to buy somewhere to allow you to fly outside of battle that costs roughly 100-200k. it means if you want that quick traveling ability you have to pay for it up front.
lastly to actually argue against something that shouldnt happen, no exp share or at least not the same strength it had in handheld games. people may hate my opinion on this but making it easier to train a pokemon in any way aside from a small exp boost here and there is asking for trouble. for simplicity trainee is the pokemon being trained, trainer is the pokemon being used, and enemy is one of the pokemon being fought.
if it is put in it shouldnt work on a trainee with more than a 10 level difference from the trainer. i say this because exp share was used in a few games to allow easy/fast ev training of multiple pokemon, as well as faster access to areas that would give more money. it makes it too easy to train in higher level areas without the risk. it can also be a potential disaster for ev training if you forget your trainee has it on before being fully trained... i have done that before in one of my games... of course if it is put in and limited the way i suggest the trainee should still gain exp the exp already gained from seeing an enemy and not fainting although that extra exp should be capped to a certain extent if exp share is working.
sorry for the long post :)