I'm quite confident it was the MT90. I spoke with a few others around the globe that had the same issue (one in UK & US). It is not immediately apparent. For the first year or two, shifting felt fine. The synchros simply wore prematurely. It came to the point that I had to resort to ATF to prolong rebuilding the box for a year or two.
It may very well be something else at work, but given that fresh rebuilt transmission lived & died on MT90, I'm not down for another round or willing to recommend. If I were to buy another MR2 & it had MT90 in it, I'd change it immediately.