I like them both, separately, and for different reasons.
I grew up reading the Marvel Comix version. I remember waiting (forever it seemed) for the Matrix quest to follow through. I really enjoyed the writing in the latter issues, and I thoroughly enjoyed how Spike and FM ended up together. It seemed to fit.
Later, I got into the Japanese ideology. Little robots controlling bigger bodies (transectors) makes since. Also, as you follow the Jap story lines it leads to the Pretenders and Brainmasters. However, the Jap's have a weird since of loyalty. I mean the friggin' blew up Sebertron! How stupid is that. That still really bugs me...however, that is another story.
All in all, I still lean towards the Marvel Comix version. Then I turn a switch in my brain as I play with the Jap toys.
Go figure.