I gave this subject way too much thought when I bought my Domino. I consulted with several guys, three who own both versions (two of who are members of FOG) and Festool USA. This is what I learned.
Both tools are great. However, the ability to recess the "paddles" on the new fence is liked very much by everyone. Especially if you use pencil lines to mark you're cut.
I was told that the pins do sometimes get in the way and can push ever so slightly the tool away from the work, leaving room for misalignments.
Glue can collect on the pins if you are not careful.
The new fence is all set for the 4mm dominos. No filing.
With the addition of Rick's MGS you are getting the best of both worlds. (More $$$ though)
And lastly, according to Festool USA the new fence has been tweaked to a higher tolerance to avoid the horizontal alignment problems that some have experienced with the pin version.
The three I talked with who own both tools prefer the new fence, and that's what really made up my mind.
You can't go wrong with either, but this is why I bought the new fence design.