I don't think many would approve of you here. We all like to play the games on our 3DS/2DS/DS and play properly.
Just so I don't come off as completely rude, no if I recall you can not transfer your pokemon from Rom to Rom.
A DS Emulator barely works, so online compatibility just does not seem in the books. They would need to configure
the entire architect of the actual console they emulated which would be a VERY tedious task.
I recommend you go buy a 2DS($110 CHEAP) coming out 12/10/13 which is same as X and Y. They might not be
as attractive as a 3DS but wouldn't you rather be able to play with everyone on this website and trade with
each other?
A good reason why getting a 2DS would be good is they will be coming out with a Pokemon Bank in about
December if I recall, which WILL allow you to transfer pokemon to each game. Problem is, you will need
to start the game again.
Anyway, I hope you can find money to buy a 2DS and X or Y.
Emulators are unpredictable, restrictive and
you can't carry them around with you!