I definitely prefer AAs over 123s or any of the other "specialized" batteries on the market that high performance flashlights use. My preference has nothing to do with performance though. It has to do with convenience because one other obsession in my life is photography and all of my Nikon camera equipment uses AA batteries. Whenever I travel, I take at least one light and all of my Nikon equipment with me and thus, AAs are all that I ever need when I'm on the road.
Agree, and you have a key point.
Yes, I greatly prefer AA over CR123. And I have a Surefire 9P with a Malkoff M60, one of the better lights that use the CR123 format. I've had a long experience with high performance flashlights, dating to the early Surefire and Streamlight incandescent options.
Set aside the context of flashlights. If you invest in some of the outstanding Sanyo Eneloop AA's, and a good charger (Maha C9000 for instance), you have batteries to power radios, lights, cameras, a wide variety of battery powered items one might want in a power emergency. And the Eneloops provide you with a very low cost option if you use them to any degree; cost per watt, the lowest.
Low self-discharge (LSD) nickel metal hydride (NiMH) batteries are the best choice out there for portable power. They are reliable, inexpensive in use (after an initial investment), and powerful. I have C and D converters to use AA Eneloops in a couple of devices needing that format, and they serve pretty well.
Back to the context of flashlights, you have LED based single AA choices like the Nitecore, Fenix, and JetBeam, amazing performance from similar 2xAA lights, and now the big 8xAA Fenix TK40 (my new "wow" light, too).
Even in the flashlight junkie world, AA based lights are right up there in performance with the exotic lithium choices, both primary and rechargeable.
If you need/want primary batteries, the AA format L91 Energizer lithium is a solid performer. Adverse reports on their safety and performance are far less common than those about the CR123. I keep some of them put away for special situations. They are priced pretty close to the CR123's, especially at retail, and have similar features for long shelf life, weight, etc.
If you do decide on CR123, avoid the uncommon but widely touted $1 variants. Stay with name brands only, and expect to pay more like $1.50 even when ordering online at the best possible pricing.