Also, I know this next idea will never be implemented but I think the C-Store should have an alien registration option to register the species you make. Why? For two main reasons: because it would be cool for the creator, and also if the creator wanted to call up another one of the species they made it is a lot easier than writing down and re-entering all the specifications by hand every time, especially if the species is super detailed. Plus, I've seen some really cool aliens that people have made out there that I'd like to add to my crew.
The problem is fitting the odd part to the other odd part. Some things wont go well together. How to put Ferengi ears on a Caitian? I kind of shuddered just now at the thought. That said, putting an alien customization pack adding in the new races parts that can fit together in the C-Store would justify the costs of the art team's time to make it happen. In fact, my hope is the surge of income you get from Caitians and other C-store purchases will allow an expansion of the art team; after all the designers design, but the hardest work is making their designs look good. The art team is the most time intensive part of the work if I'm not mistaken.
I support adding the bits of all custom species you buy into the Alien generator and I also support separate alien bits packs.
However, I also think we still need some more basic-game stuff on the Alien generator, especially the wider selection of horns seen on some NPCs and full parity between male and female alien options*.
While we're on the general topic of C-store species, I'd also like to see every factions' species available in the C-store to use in other factions. Defectors, adopted orphans, rebels, and the like are all interesting character possibilities.
*My personal peeve is the same one eventually addressed in CO - there are face tentacles for males but not females!
I'm a bit confused by the limited choices in the alien creator. Not to say that you can't make interesting aliens, but that it seems like some pieces have been purposely withheld. For instance, there are Hirogen pieces in the alien character creator, but not for every category, only some of them. And that's odd, because there are Hirogen NPCs in the game that appear to have all the Hirogen parts. Why?
And, yes, if you purchase a new species from the C-Store, its parts should be added to the pile in the alien creator. It's unpleasantly surprising when they're not.