I haven't used the MMP-E active cable, but I run 4006C's with the compact preamplifier MMP-C and the DPA low-profile XLR cable.
I haven't done or heard direct comps between MMP-A/MMP-C/MMP-E, but there are some spec differences, as I'm sure you are aware if you've looked into this. Between MMP-A and MMP-C, MMP-A has slightly lower bass extension, slightly greater dynamic range, slightly better external noise rejection. There are the same differences again between MMP-C and MMP-E, with MMP-C having the better specs compared to MMP-E.
So if size did not matter (and we all know it DOES!), you would probably choose MMP-A over MMP-C and MMP-C over MMP-E. But I have read that certainly the differences between MMP-A and MMP-C are quite subtle, and that changing the grids or APE's on the 4006's has a far greater influence on the sound than the choice of preamp.
I suppose the differences between MMP-A and MMP-E might become more obvious in a head to head. So I chose 'C' over 'E' so that those differences would be minimised, whilst still retaining the small form factor.