Despite these positives, I believe there are two major flaws -
A cruel, thoughtless, and unnecessarily sad ending, both to Eragon and Arya's relationship, and to the series in general. Eragon's reasons for leaving were weak, but Arya's reasons for staying were...weaker, to put it lightly. Even so, I thought the ending was touching, in a weird sort of way.
Secondly, too many interesting and crucial plot points were left unexplained. The Menoa Tree, Tenga...the list goes on and on.
However, if CP writes a future installment (book 5) wrapping up all the plot lines and allowing a more satisfactory conclusion to Eragon and Arya's relationship, my opinion would drastically change. If we find out that Eragon is somehow able to eventually return to Alagaesia, I think Inheritance would shine as the best book out of the Cycle.