Hmmm.... Here's my take on this: About the only thing I can think of is weight (if you are an "ounce Nazi"). A flat-top plus carry handle is heavier than an A2 upper by a handful of ounces...and an A2 upper is heavier than an A1 by about the same (I know there is a post by me around here somewhere that lists the relative weights of Bushmaster upper receivers...). So, if you are the type that wants to build a super-light basic carbine (A1 upper, BM superlite barrel, 6-pos stock, and forget about all the "H-buffers, fancy grips, dreaded double heat shields (too much weight., right?
), etc.,) then a flat-top may not be for you. But, if it's your ONLY rifle, you may get the dreaded "flat-top" envy from time to time at the range...or if you hang out here "too much."
That said, if weight really does concern you, rest assured that the "extra" weight of a flat-top with carry handle or optics is usually centered on the receiver and it doesn't effect handling much.
All this aside, I have my 14.5" flat-top + BUIS/M2, 93A stock & Colt M4 handguards...as well as my FF 17.5" flat-top + Leupy "SPR-ish thingy", and now...yes...I am looking to build a K.I.S.S. A1 uppered AR-15 with a 14.5" barrel & RRA 6-pos stock for a light & fun little plinker.
YMMV.