Starting with tf capable characters - There's an option to not start with them and instead have a random set of characters, the default is just so transformations are accessible early.
Realm Shaper - It's primarily used for expanding the realm, which gives you more empty land (building slots). It's also needed for a couple of missions.
Essence Warper - There's actually a lot locked behind essence warper and the Ritual Ground upgrades (fusion and most species changes amongst them); it isn't useful for regular tfs but there's a lot that need it (it might actually be overloaded).
Monster girl races - Yeah, they're a bit thin; they were content additions for a while but need some more features. I have some interesting ideas for robots (and some variants off robots) for later but it's something that generally needs improving (when I get to it, my list is huge haha).
I've made a couple of notes based on the other stuff you've mentioned, thanks for all the feedback :)