VCM can either be disabled by VCMuzzler/VCMTuner, which is cheaper but less "proper", or a KTuner tune, which is more expensive but more stable. Personally, I think you should only go with the KTuner if you are going to do other tunes anyways.
That and they are usually 60+ pounds heavier than the manual transmission version.
I find it a little strange when I looked up and found out that, according to Car and Driver, 6-6 is 0.2 seconds slower than V6 AT in 0-60 time. Usually, MT Accords have more aggressive gear ratios, and like you said, they are more power efficient and lighter.
That said, with some more performance cars like modern muscles, ATs are indeed faster than MTs. Take Dodge Challengers, for example, the 8AT version has much more aggressive gearing than the 6MT version. The first gear ratio on the 8AT of 392 SRT is about 4.7, while the first gear ratio on the 6MT is about 2.9. I would still grab a MT if I have to choose, though.
My first car!
2008 Honda Accord Coupé EX-L V6 w/Navi 5AT PMM
Mods and such things:
AFE Pro Dry S drop-in filter
HFP body kit
RGR-16D HFP Alloy Wheels
i-VTEC & 3.5 stickers
High and Low beams - Philips CrystalVision Ultra
Front turn signals - HV 6000K white/amber switchback
Rear lights - Philips Vision LEDs
Crosstour shift knob
OEM footwell lights
1999 Toyota Corolla CE 5MT
2009 Mazda RX-8 GT w/Navi 6MT