The throw animation isn't fixable without major work and we haven't figured out how to change the in-battle animations yet. it's frign hard.
You can't really make it "start" with the hightest flag, but you could make a pokesav file with it.
Modding the pokedex is also, for now, limited. we can change text, but the locations are pre-programmed, and it is a extremely high amount of work to change all of those, and we don't even know yet how to do it.
I still work on my patch, even though bloody diamond is long long dead.
If you have suggestions for me, you can forward them via PM.
If you want a link to my patch, I will not put it blatantly in here, you can pm me too.
The list for bloody diamond was being done by me but I stopped doing it because I developed my own hack. There is currently no list and I doubt anyone is in process to make one.