About your first point, you're talking about shadow clones. Shadow clones are copies of your own self, so the chakra signature in each clone is the same, and hence Neji was trolled. That's not the same as a transformation jutsu, with which you pretend you're someone else. A transformation jutsu merely masks your outward appearance, but it can't change your actual inner chakra.
Your second point kind of discounts the fact that Kaguya's had her byakugan on, and byakugan users can't be snuck up on. She should have seen Sakura coming, although, yeah, she was distracted by Naruto/Sasuke/Kakashi. Still, Kaguya could have just teleported to another dimension again, like the Super Gravity or the Ice world. Even if Sasuke has amaterasu, it would have bought her just enough time to not be sealed. She just didn't do it because plot.
Third point, she should have made some clones then. Why is it that the only offensive moves this ***** knew were chakra punching, bone-throwing, and hair whipping? The final villain had three moves? Unacceptable, she obviously understood jutsus and how they worked judging by her analyses, so she should have been able to copy shadow clone from Naruto with her cracked out Sharingan.
