I totally agree that for me the main storyline will always be Regeneration One. Its part of the story that got me hooked all those years ago as a kid. Marvel Transformers made a huge impression on me & is the main reasons why I have been interested in it all this time.
Personally I think Regeneration One is a great comic, I'm really enjoying it. The pace is slightly slower than the old comic but I think that it works on the whole. Its nice to read about the same characters we knew over 20 years ago, this is the Optimus Prime I grew up with.
I still buy MTMTE but I personally find it a bit hit and miss. I'm not thrilled by the humour and tone but I know that many hold it in high regard. Having said that I still think there have been some interesting stories so far. Of the two IDW comics though I prefer RID. However Regeneration One will always be my favourite because it is a continuation of the orginal story. The story that was so influential that we still talk about it to this day. For me it will always be "The" Transformers comic.