I should state that this is my first pool and first pool season so my experience is limited.
We bought the auto cover to keep our kids and pets safe. The side benefits being limiting chemical use, reducing evaporation, virtually eliminating debris in the pool and heat retention (all though I was told a bubble wrap blanket works better for this).
That said I only uncover the pool to swim or run the polaris. So my pool has been on average covered for 20-22 hours a day (except on weekends where we may swim longer but still cover when not swimming/running polaris).
What I have noticed is that with the pump off and pool covered on sunny day, when I open the cover and start swimming the top 12" of water is super hot, and the bottom couple feet is noticeably cooler. With the pump running while cover is on and it is sunny, when i uncover and get in i don't notice this layer of superheated water. I my a comment to the Coverstar rep about how hot our pool was and he asked me when my pump ran. At that time it was running 24/7, I told him and he said that's why it's getting so hot. Then he explained to me what I've now discovered on my own. If i want to heat up the pool run the pump with cover on and sunny causing the water at the top that's getting so hot to circulate bringing new water to top to heat etc. If i would like to minimize the heating on sunny day with cover on turn off the pump so that the water doesn't change out below covers surface.
Unfortunately at this time i have no experience without the cover on, but if my pool keeps getting hot I might have to start leaving it uncovered during the sunny afternoons (because i think it would be more apt to not heat up as much without cover), but that may indeed be completely wrong as Jason mentioned above baring wind conditions.