Two things: the first one being bouyancy (and being horizontal) and the second being gear choices.
Everything we did was kneeling on the bottom of the pool or ocean. That doesn't help your buoyancy at all because you obviously have to be negative to stay planted on the bottom....and it doesn't help you figure out trim at all because you can't swim forward while completely vertical. I wish we had practiced all our skills (mask removal and replace, regulator retrieval, air sharing, ascents, descents, etc) in a horizontal position, since that's where you want to be most of the time.
One of my biggest complaints is that all the instructors and DM's were decked out in the same gear....which included jacket BC's, split fins, and "standard" length hoses. I wish we had been exposed to different types of gear and configurations, and then been able to pick what we wanted based on our diving goals, rather than based on it being the only thing you've ever seen. That was definitely a "lesson learned the hard way"....bought all the wrong gear (for my diving) the first time around, and had to try to sell and buy new gear within a couple months.