I think that, like Soldjermon says, everyone has their own opinions of both programs. I'm one of the ones who use both programs, but for different reasons.
I use PokeSav to add the Events into my game, while I use PokeGen to make pokemon to battle online with.
Sure, PokeSav has different options to edit more than just pokemon, like the Events and items etc, but while making Pokemon with PokeSav, it doesn't fully help a user when making one like PokeGen does. PokeGen is by far the better Pokemon making tool, Codr has done a spectacular job in making it, plus it is updated regularly and he takes in user opinions. Not slanting COM's work with PokeSav because that tool has helped hundred of people, but in my opinion, in terms of making Pokemon only, PokeGen wins hands down.
It has a very friendly UI and is pretty basic to understand how to use it, for example, moving the arrow over something like the nature brings up every nature and which stats are helped and hindered. Now if PokeSav was to have more features like this, then perhaps my opinion would be altered, but for now, I'm sticking with Codr's program.