I'd suspect we'd keep Glitches seperate from Pokemon in the breeding, so no half-breeds. I like the idea of single-celled organisms, but they'd probably reproduce sexually.
But the idea of a new species... Well, that gives me ideas. What if not all Glitches could be found in the wild? Maybe it would end up being a sort of subquest, to get all of the Glitches through breeding and catching.
Just something to think about.