Do any of you ever hear any complaints with a two stage a/c systems?

Our home has a two stage system installed and my wife tends to complain about the long run times. The system seems to run for extended periods of time even when the thermostat temp is satisfied. I guess we are just used to the way a single stage unit cycles and just have not adapted to the way the 2 stage system runs for such long cycles "for enhanced comfort".

Our home has considerable wall/window space facing the unshaded west afternoon sun. We have planted trees, but they are still growing and need a couple of more years to provide good shade. When the a/c runs in stage one even with the airflow set to high or 450cfm per ton, we do not seem to get enough cool air on that side of the house to keep the temp even. The west side of the house may be 4-5 degrees warmer than where the thermostat is. When the unit is running is stage 2, the airflow is higher and the temps are much more even throughout the house.

I know it would be possible, although not an ideal situation, to have an xl16i systems wired up to only run as a single stage unit, more like the xl15i, eliminating stage 1 completely in order to achieve operation like a standard 3 ton a/c? Would it harm the OD unit to only run in stage 2?