>>19820822Some of them will, depends on stat distribution, abilities and moves, since quite a bit changed in-between the gens. Whether yours will, hard to say, but give it a go, not like you have anything to lose, right?
The problem is that once you have a Pokemon that has something odd about it by newest gens standard, you cannot really use PokeGen to edit it, since that program only supports gens 4 up to 5.
You'd have to use PokeStock, edit the save file, figure out what's wrong, then send the Pokemon from gen 3 to gen 4 by normal method, cross your fingers and hope for the best.
For the purposes of just completing your Pokedex, it's easier just to create gen 4/5 Pokemon in PokeGen from scratch and have the game treat them as if they were born from an egg.
But if you really want to transfer your old bros, you can give it a shot. It's just that it would be easier to recreate them as opposed to transferring.