Like any other decision, there are pros and cons. This is how I see it:
Pro:
-You don't have to worry about those pesky time limits for Steps 1-3 required by some states.
-You don't end up taking Step 1 only to have it "merge" with Step 2 a year or so into your PhD (note: this has been discussed for awhile, but there is no definite date to speak of).
- You get to enter MS3 with your store of medical knowledge still fresh in mind.
Cons:
-You waste time that could have been used for a research rotation (don't underestimate the value of that second summer and potentially MS2 year).
-You get to go through MS2 with a slew of people you don't know.
-You really don't have enough medical knowledge to apply it to your PhD in any meaningful way - it may sound idealistic, but isn't the point of MD/PhD training to provide a medical perspective on basic science research?
-Your "return to med school" date is set in stone. You can always enter 3rd year clerkships a little bit late, but you need to be present for required MS2 exams and courses from the beginning.