I'd put 6" x 9" speakers over 6.5" rounds in a heartbeat. The larger cone area lends itself to better low frequency sensitivity. If you'd like "deeper" bass, then it would be a cinch.
A friend summed it up exquisitely...
http://www.diymobileaudio.com/forum/car-audio-truth-myths-industry-dogma/103078-myth-oval-odd-shaped-speakers-cant-sound-good-round-speakers.htmlWhen I was heavy into IASCA competitons in the late 80's, very few people knew how to make a decent sounding automotive system (or boat systems). Higher end autosound components were extremely high-priced, hard to find, and our choices were limited. None of us would have ever dreamed of trying to make a 5" speaker reproduce anything below 200Hz. We'd usually tweak the active crossovers to sharply roll off at ~160Hz on 6.5" speakers. Decent 6" x 9" speakers could be relied upon for frequencies down to 100Hz, and since most cars back then had 6" x 9" cutouts on the rear shelf, it was a no-brainer. Physical limitations of a smaller cone make them inherently incapable of reproducing bass as efficiently as a larger cone, just as a larger cone is inherently incapable of reproducing high frequencies as compared to a smaller cone. One doesn't try to make a 5" speaker work as a tweeter for a reason.
Sound quality was an important factor that the judges looked at. I never heard one of them comment that 6" x 9" speakers were somehow inferior. Quite the contrary in fact; the extended reach into the lower frequencies helped complement large subwoofer systems that tended to be too "peaky" in the double-digit frequency range. They'd fill in the gap between subwoofer and midrange quite handily, and their scores in the sound quality aspect of the competitions tended to reflect that fact.