Gotenks could go SSJ3 because Goku gave Goten and Trunks the demonstration before they fused, Vegeta didn't see SSJ3 before he became Vegetto so he (Vegetto) didn't know how to ascend that high, he only goes to SSJ2. Goten and Trunks knew how to ascend to ssj3 but didn't have enough power to do so, when they become Gotenks they have the knowledge and the power.
Mystic probably wore off, It wasn't a standard form, he doesn't use it after Movie 13 and in the years of peace that followed he didn't train, so he either got weaker, lost the ability or both. In Buu's Fury the Mystic form slowly drains away (but never dissapears fully) so it's not a completley unsolicited idea.
As for Goku staying as a child, I personally think it was his sense of loyalty as a protector of the earth, if he's younger he can live longer because he can age all over again, so he can defend the earth for longer. And the point Shao made. I did feel sorry for ChiChi though. When he was wished smaller, his power did decrease but not so dramatically that it became like it was in Dragonball, he would never have lasted against Baby like that.
Of course Vegeta skipped SSJ3, he didn't know how to do it, and he cheated to get to SSJ4, having Bulma build a machine to do it for him, what happened to his pride?
Super Saiyan 4 is the perfect saiyan state, it takes the best of the normal form and the best of the oozaru form and puts it into one body. It retains the 10x power boost of Oozaru while not being a slow massive target. Because it's designed to be the ultimate saiyan form, I imagine it changes the transfomer into the perfect fighting age and size. He gets a long reach for punches and kicks and doesn't diminish energy from being old. That and the fact that if he was a small SSJ4, he wouldn't have been able to fuse into SSJ4 Gogeta so Toei would have to change the script. Lazy
See? GT doesn't have that many plotholes, you just have to think of ways around them. *accepts back payment from Toei agent*
[EDIT: Thought; when Goku shows Babidi the SSJ3 trans, the camera goes into Goku's eye and you see Goku as an Oozaru, Goku as an adult and Goku as a child, maybe this was hinting that it's the last form before the ultimate one?]