This project is Create-A-Pokemon. I personally take that at face value. Let's create a Pokemon. That should be the only variable as far as I'm concerned. Not an attack. Not an ability. Not an item. I feel like we should play with the parts that Gamefreak has in the game and only those parts, and make a competitive, interesting new creature out of them.
Beyond that, by keeping to that, it keeps this as new player friendly as possible. Explaining a new Pokemon is one thing. "He's a Bug/Ice sweeper type." Having to continue that and say "He's a Bug/Ice sweeper type of Pokemon with this awesome new ability that means that he's immune to rock type damage on the switch in" is a whole 'nother thing. There's a lot bigger chance of someone saying "F this, that's dumb, all you guys are dumb" the more stuff we make stuff up.
If this was Create-A-Metagame, then I'd agree with you. I wouldn't like the purpose as much, but I'd agree with you. But we're inserting new Pokemon with the intent of modifying the metagame piece by piece. I think it should just stick with the Pokemon, and let them do the work.
That's my general opinion.