I've recently gone through a very thorough bio-mechanical assessment with a podiatrist who advertises in RW - and is an ex-GB international middle distance runner.
I've been precribed orthotics (and picked them up last night) to help deal with a leg-length difference and over-pronation.
I asked him about neutral vs. motion control shoes - and his view was if you need motion control without orthotics then you need motion control with orthotics - otherwise it is like using a corrective stable base on an unstable surface such as sand.
Logically this sounded sensible. I tried the orhthotics out walking in two different pairs of running shoes - a stability shoe (Saucony Grid Hurricane) and a neutral shoe (Mizuno Wave Creation). The control was markedly better in the former, where the excessive rotation in my right foot was eliminated - which seems to bear out what he was saying (for me at least).