Long term, it might be better off, though - the NYCTA decided years ago that quads and longer were better than singles or pairs, for a varitey of reasons.
For one thing, going to a quad config would get rid of 2 cabs, and two cab's worth of junk to maintain. It'd also allow one to distrubute the equipment around over 4 cars, which would have advantages. Plus, you'd get rid of one coupler setup.
Actually, I think an A-B+C-D....C-D+B-A setup would be best - you could design the equipment to be much more optimized for it's job. Right now, every M-7 has to be a cab car or a middle car. That's not only a disadvantage from a weight standpoint, but it means lots of unused equipment that needs to be maintained, plus you have to design the car end to allow safe pass through AND be good in a collision. This isn't easy, and it's not optimal. If you could totally eliminate the end door, the cab structure could be significantly lighter, yet stronger than the existing setup. plus, mid train cars wouldn't have a cab - they'd have extra seats.
Yes, I realize that from a shop standpoint, this isn't ideal, thus I'd propose making the end 2 units linked, then having the inter-train cars be a married pair (effectively - end units would be an A-B pair, mid units would be a C-D pair). Thus, you'd still have 'pairs', but they'd be designed more for their position in the train. This might be a better compromise.
The arguements against generic married pairs are numerous, but the arguements for them aren't very big anymore - the LIRR doesn't (and probbably can't due to FRA), make very efficient use of joining/splitting trains, and there's little or no redundancy that the arrangement adds - just more stuff to break. Elsewhere in the world, married pair EMUs aren't very common anymore (though married triples are), except for lighter 'branch line' stuff. Really, if it weren't for the FRA and all of the LIRR's grade crossings, pairs would be just fine. But the FRA's not going to grow up anytime soon, the LIRR has lots of grade crossings, and that makes the economics of A-B pairs a bit suspect, since most of the cars in between the end cars have equipment that's unneeded, but requires plenty of regular inspection and maintenance...