Ion engines are great if you use them correctly. Otherwise, just don't use them.
They have a TWR of 0.2, need lots and lots of electricity, and their fuel is very hard to get more of.
But, they have lots of Delta-V and Isp and aren't that heavy (1/12th the weight of the NERV).
Of course, the electricity is very hard to get after Dres, meaning they are better suited for the inner planets.