eric,
First, the best angle of climb speed for the Super Cub is 45 mph. The configuration recommended for that performance maneuver is full flaps.
Full flaps and 45 mph in a Cub provides a pretty "interesting" attitude, but that's what will get it over an obstacle if it's tight. Of course, if you've needed that sort of dramatic launch, you probably screwed up in the first place.
Note that that is all Vx--which is purely obstacle clearance performance. That isn't, in my opinion, the best way to get underway on a regular basis. Note that if you experience a powerplant failure at that pitch attitude, the airplane WILL stall before you can get the nose over. If that happens close to the ground, it's going to be a little ugly. So, I demonstrate this at altitude, practice it, do it a few times on takeoff, then tell students to use this technique only when you really really have to get over an obstacle.
As to using full flaps on a "normal" takeoff, I generally don't. If you want to launch really really short, you can practice starting the takeoff run with half flaps, then pulling the flaps to full, airplane fairly level, to get it airborne, then smoothly retract the flaps to half right after takeoff. That technique works, but it takes a good bit of practice before it will shorten your takeoffs much.
As to landing, there shouldn't be any issue landing with full flaps, even empty. What do you mean you almost learned the hard way? I don't understand what you mean by "running out of elevator prior to the stall". If this means you have the stick at the aft stop and the airplane still hasn't stalled, so......? Please explain a bit more explicitly your concern.
Most folks who are landing short are working power against drag to get teh airpalne as slow as possible, and therefore, most very short field landings are accomplished with some power on right up close to or into the touch. REmember, power ON stall speed will always be a bit slower than power OFF stall speed. Distance on landing is primarily a function of how much energy (speed) the plane has remaining when it touches.
MTV