It makes perfect sense. Right now the best way is to always keep the user object is a (semi) global variable that you can access from all of you're controllers through a MY_Controller or similar.
I have some plans for an updated group of methods that will solve the optimization issues, add more logical and OOP style methods and add a bunch of needed features but haven't had time to write them all yet. Just know that they are coming soon.
The meta update issue will also be fixed in the new update method.
Sorry I can't give you any kind of timeline ATM though as my life is crazy busy right now.