I realize the thread is a little old, but I just saw it and figured I'd chime in.
As the OP undoubtedly knows, each branch of service has its own SA (with the exception of the Marines, who use USNA).
Also, as I'm sure the OP is well aware, USMMA grads may enter into any of the branches of the Armed Forces. A graduate of the school will be judged as all other officers are. That is, the officer's success or failure will be based on how he or she performs on active duty.
That said, there is no doubt that service-specific SA graduates get a proverbial "leg up" when they come out of the gate in their respective branches. This is something that is usually not as readily available to ROTC/OCS graduates. By "leg up," I mean that they will have been immersed in the service's traditions and culture more than the ROTC grad, and will have a much larger network of people on active duty on which to rely. I would imagine this exists to a smaller extent for USMMA graduates in the Coast Guard and Navy, as I assume that is where the bulk of active duty commissions go for KP. For the Army and Air Force, I think the "leg up" (in terms of alumni connections etc.) would be a bit more negligible. I am a VMI graduate who went AD in the Air Force, and I never met a USMMA graduate. This doesn't mean they aren't out there, of course, but it would appear that they are in smaller numbers with respect to that branch of the service.
Still, if you are going into the Navy, the "Academy" you will hear referred to in conversation with your shipmates is the one in Annapolis. If you go into the Air Force, it's the one in Colorado Springs. Each service thinks of its own SA in that regard, and yes, I'd say it is a source of advantage. I don't think such an advantage carries over entirely for USMMA, or if there is some degree of it, not to the extent that it does for the service-specific Academies. In the U.S. commercial shipping fleet, however, USMMA is the gold standard.
All this considered, this is just the answer to the OP's question on a general level. There are great officers and lame-o officers from each of the commissioning sources. I've had Wing commanders from USAFA, OTS, and ROTC...there were good and bad from each source. In the end, how "active duty" views your school shouldn't be the principal concern. The principal concern should be how your chain of command views you, the individual LT, by how you accomplish the mission and take care of your enlisted folks.