There are still many fundamental problems with the string theory and its successors (M-theory etc.). I mention just three problems which a good Theory of Everything (TOE) should solve:

1. A good TOE should be able to formulate its own principles and fundamental equations. Moreover, these principles and equations should clarify and simplify our picture of the physical world and allow some testable predictions. As far as I know, nothing like that is still available for the string theory (M-theory), in contrast to its rather long development and far-reaching claims. 

2. A good TOE should allow  calculations of all interaction constants and particle parameters from its fundamental principles. It was actually one of the original Einstein's goals - to give some purely geometrical or mathematical origin to fundamental physical constants. No variant of string theory is able to calculate these parameters from some first principles.

3. If the TOE is formulated in some space of higher dimension (11, etc.), as expected, there should be also a unique and justified principle of compactification - e.g., a principle how to project the structures from the 11-dim world to our tangible 4-dim world. In its contemporary status, (super)string theory is very fuzzy and umbiguous concerning the compactification.

 
In my opinion, the very word "theory" is rather premature in connection with the (super)string theory and Einstein himself probably would not be very happy with its present form and claims.