Its a matter of comfort, not efficiency. The two stage will cycle fewer times and maintain a more even temperature with smaller swings. The variable speed blower will be much less obtrusive in its on/off cycles, ramping up to its run speed and ramping back down. Easier to adjust to the correct CFM for a specific installation as well. The Trane and American Standard furnace/AC are generally the same as are from the same manufacturer although each has some models the other does not. Our AS unit with 2 stage furnace, 2 stage AC and variable speed blower has worked well and uses considerably less electricity than the 10 year old Bryant on the other half of our home.

You may be misunderstanding the terminology. The term "variable speed" refers to the blower in the furnace. So, it is possible to have a single STAGE furnace, with variable speed blower. Your typical (older) furnace may have a multi-speed blower. where the installer 'selects' the required (single) speed through electrical taps. Further, in the above case, the speed of the blower is not variable (i.e., you don't have a choice of fan speed, while heating. As with any gas furnace, the fan speed must be selected, such that the air flow through the furnace will produce a temperature difference (known as temperature rise) of the return air to the outgoing air, within specified limits. What a VS blower WILL do is ramp up in speed if restrictions (clogging filter, poor duct system)prevent the selected airflow from flowing. It will (with proper thermostat) reduce airflow in cooling to increase dehumidification. A 2-stage furnace (also available with VS blower)and proper thermostatic control, provides greater comfort from having longer running cycles. NOTE: A 2-stage unit provides greater comfort, not greater efficiency. Carrier/Bryant produce a 3-stage furnace, which they refer to as 'modulating', but there are larger gaps in output between stages. A modulating furnace provides many stages of heat and utilize variable speed blowers. Again, the ultimate in comfort, but not more efficient than a single stage unit of the same AFUE. You should note that newer furnaces blow a lot more air than older units of the same size. Combine that with a VS blower, if the duct system is not sized for the airflow, the system will be noisy and efficiency may suffer. So, proper sizing and duct system analysis is essential. On a personal note, I replaced my oversized SS furnace with a Rheem Modulating unit (13 stages). Before changeout, the upstairs was always cold; the downstairs would warm, but would chill before the unit would restart. I had to use a space heater in an upstairs bedroom (computer). Now, I have relegated the heater to the basement, and frequently sit at my computer in short sleeve shirts. Insist on a manual J (heat calc) and duct analysis. V

aab what area of the country do you live? both of these are nice furnaces. with the two stg XV95 Trane, you need one of the following two stg stats; Trane's 803 or identical HW Vision Pro Mdl or HW Vision Pro IAQ. With the Carrier three stg ICS furnace, you must have the matching Infinity controller-no substitute. You don't want to cripple either of these furnaces with the wrong stat. price, warranty, and comfort with the dealer would drive my decision although Carrier with the Infinity controller would be my choice. what are you doing about either an AC or HP condenser? IMO

I'm also in the Bay Area and presume the OP has PG+E as I do. Gas and electricity charges are tiered by order of the PUC, a so-called "baseline" allowance for the first small tranche and then the "excess" rate. For me, the baseline is enough for water heating and cooking and was $1.19 per therm on my last few bills. The next tier, immediately reached in any month when heat is used, is $1.75. Yeah, it's high, compared to rates elsewhere in the country. I replaced two systems a few years ago. The HVAC contractor recommended sticking with 80% furnaces because he said there would be no payback for the incremental cost of more efficient ones, so that's what I did. I guess it depends on how warm one keeps the house during the winter. We tend to stick to the high 60s, with daytime and nighttime setbacks, and in a larger house than this one. I don't think I've ever spent as much as $750 per year on heating and it's usually less. To save 10-15% isn't going to get me very far any time soon. Also, because of the mild temperatures, single stage units seem to be the most common. HERS testing is required for all HVAC equipment replacement and installation jobs. It's basically testing by a 3rd party, not the HVAC contractor, for duct leakage and requires reasonably easily located holes be patched. For my job, I had them do a complete rehab and reinsulating of my old hard duct system anyway, and in advance, so the HERS testing was a non-event. But it does cost about $1K.