Also folks act like Incarnates are some beast that is inevitable for every level 50 or that they are something that you can't work around.
Team leaders can do as you mention and also ask incarnates to unslot those powers. (They can actually be unslotted easier than enhancements, and changed to different powers easier than primary/secondary/pool powers). And if you (in general) don't even like the system, newsflash: don't craft the powers!
I bet you money though, as you alude to, many more folks prefer incarnates as is (including using them as they see fit in ALL content, at ALL levels), than those that would be willing to unslot them. I don't consider this a problem that needs fixing at all.