High thrust line did not seem to be as big a problem as the critical angle of attack required for landings. The basic rule on adding power is that when you push the throttle forward, with the other hand you pull the yoke back. Always.
Angle of attack is a non-forgiving issue. Too high, and the Lake will ricochet back up in the air with a steep angle of attack. It is not really like a bounce. What happens next to the unwary pilots is they add full power, and don't pull way back, and the thing nosedives. This has been the end of more than one Lake, including one on the Cheaspeake Bay that was used for Lake checkouts.
Angle of attack too low, and the Lake will plow into the water, and can be turned over on its nose. Again, adding power to fly out of that mess really requires a fine touch on the yoke to get a slight climb, rather than dig the nose in deeper and have a high power upset.
I had a ball flying the one owned by a friend and advanced student of mine, who had a CFII rating and lots of experience flying Mooneys and Cessna 206. He scared himself to death up on the lake in Canada where his family had a summer place (the reason he bought the Lake). Said he was landing, glanced off the water, shot up in the air, it nosed over, and next thing the windhield was full of lake. He says he remembered me saying over and over, push with the right hand, and pull with the left. He recovered it, flew 20 miles to a long paved runway, and would never let my fly it on the water again. He replaced it with a Piper Aerostar, to fly to Canada in!
By the way, the Lake company training at that time said that if you do glance off, just hold the wheel all the way back, don't add power, and let it come down on the hull. Now don't you know that would loosen a few rivets and jar your teeth, at best. They said this to try and prevent the power nose dive from 20 feet.
Another problem is trying to sail it up to a floating dock. Low wings and sponsons pretty well eliminate that option.