I designed a lithium ion battery charger a while back and the two biggest things the customer stressed were to ramp the charging current down in a predictable way as the very accurate peak charging voltage was approached and to help them keep the battery from being charged if it was too hot or too cold (0 to 50C was generally considered to be safe). I had to dramatically change the design late in the game to move the "refresh" voltage up closer to the peak voltage and make that voltage much more accurate...after a charging cycle finally reached the peak voltage and the charging current was completely shut off, the battery could self discharge sitting in the charging cradle or maybe discharge due to a parasitic load. If the refresh voltage level that signaled to start a new charging cycle was not very close to the peak battery voltage, a customer could take the device out of the cradle at just the wrong time and have much less capacity than they would expect.
Lack of deep discharging was not really viewed as an issue by our customers, probably reflecting that we were targeting consumer devices that would have limited lifespans. We would still try to trickle charge a battery with a very low voltage at the start of a cycle (below 2.5V), but this charging would terminate in an accelerated fashion if the battery voltage did not pop up fairly quickly...a lithium ion battery that is still alive should recover from a low voltage very quickly even with a small charging current.
The chemistry was generally viewed as being fairly "easy" except for the critical current rampdown near the peak and the super critical battery temperature concerns...no real memory effect and deep discharging also being of little concern beyond the need to trickle charge down low. Of course, I was not a battery expert and was generally designing to specs that the customer had OKed, but we had some latitude as to how we approached some things.