The games you mentioned are all A+ titles and you should play and complete them first along with one more game called Heavy Rain. That should take you quite a while. Next you should definitely have a look at the Metal Gear Solid series, Army of Two series, Killzone Triology, Resistance 2 and 3 (1 will seem extremely dated graphics wise now), Dead to Rights: Retribution and also the God of War saga. Also, Beyond Two Souls, Journey, Ni No Kuni are definitely also worth playing through.
As far as the DS controller of the PS3... yes it does need time to get used to. Stay at it and as you progress through the games you'll slowly come to terms with the control sticks and buttons. Muscle memory takes a little time to get mastered and as you play more you'll get the hang of it.