Short/missing auto stop seems to mostly be a function of the climate control and not the 12V SOC. When the climate control is off, auto stop comes on and lasts indefinitely once the engine is warm enough. It does not seem to be affected by the 12V loads of the lights (which I believe is a much bigger load than the CC fan), radio, etc. As a previous poster noted, auto stop is more affected by the need for heat than for A/C. Auto stop is more frequent and longer in the summer with the A/C on than in the winter with the heat on.
I believe this is a programming issue, the Honda engineers decided to restrict auto stop when heat is needed. Perhaps they were worried about cold occupants or the safety of defrost. It may be that auto stop in winter is counter productive, since the coolant temp lost by the heater during auto stop may cause less efficient operation or more emissions.
When running the defrost, I have observed the engine temperature actually drop from 150 to 135F when driving on a level road (ICE on) at 35 MPH, 25F outside temp in the morning. Running the climate control has a compound effect, as it makes it take longer to reach the engine temp where auto stop will be engaged, and it shorten/stops auto stop in general.
Auto stop is not a simple function of coolant temp. In the morning it takes about 10 minutes of 30 MPH driving to reach 160F or so where auto stop will engage. But if the car is stopped for an hour and restarted, auto stop starts a lot sooner, at 145F, so it must be measuring other factors besides engine temp.
Even with the climate control off, auto stop will eventually stop engaging in stop and go traffic, but it takes 15+ stops, if not more, and I believe this is caused by low NIMH battery charge, as the engine temp was still high.
In short, I don't think a larger 12V battery going to help.
2010 EX Sky Blue since 11/2/09