One side is warmer than the other = Yes , simply due to the electric components inside the charger , if you feel the back side of the charger one side should be warmer than the other , and this will translate to the batteries ..
Also due to the way the current tappers of , the greater the battery capacity , the slower this charger will be ..
Depending on how depleted your cells are , there is no reason you cant pull out the cells early , say 4.15v , wont make that much difference to run time , but it could take an hour or more for the charger to top them up ..
I am yet to see a true fast charger , unless your talking balance charger ... But thats a different kettle of fish