MS3 is way better than MS2. Both are considered better than a Hydra and with more community support. Sometimes, issues like the ones you described can be traced to tuning rather than hardware. OEM does a pretty decent job in these aspects, mostly because Mazda had the resources to support a bunch of calibration engineers fiddling around in all possible conditions.
As it regards Skunk2, here are some data from 949 Racing. Tested on a "forged, blueprinted but otherwise stock NB2, header, CAI, MS2, pump gas." This is JDM/EUDM squaretop vs. Skunk2.
"First of several test we plan to run. These runs about an hour apart.
Optimum spark table didn't change at all. VVT table changed quite a bit but resulted in about the same power. Square top obviously wanted less fuel past 7k.
Ran out of time on dyno today so we didn't try the spacers. We'll go back next week and do that. As expected, a bit more power on top with the S2, no significant gains in midrange.
What is key to note for folks who set their redline at 7000 (stock redline) is that there are no gains below that."
Eitherway, the OP mentioned ITB's and I think we universally agree that ITBs>anything!