Another option is to just put a bracket directly on the transom. Take two 12" X 18" pieces of plate aluminum and put a piece of 2X4 (or 2X6, depending on how high you need it to be; a single block of wood is better than two smaller pieces) between them at the top, slide one piece in front of and the second piece behind the transom, then bolt through both pieces and the transom. This really only works for fairly small motors, though.
You can also get a similar bracket welded up with side rails to distribute the flex (the higher you get from the original transom, the more flex you get if you hit something) into the gunwales (I attached a photo of it). I've had good luck with this to convert a short-transom jon boat to a tall-transom so I could switch out a prop and a jet unit without any other adjustments. I had the first one welded to fit either a 35 jet or a 35 LS prop on the same transom, and on a separate boat, made a bracket with 2X4s to run a LS 7.5. Both worked pretty well, but you'd want a more rugged setup for the heavier motors. running a LS prop can spray more than a SS with this setup, so making some sort of flange to keep the spray down might be something to consider.
My issues with jack plates are that they make it more difficult to drive the boat (unless you have a console). Being 4-5" further back than normal, you have to lean way back to operate them. As other posters mentioned, this changes the weight distribution of the boat. Having the weight centered over the transom, it drives like any boat would, but you just need a thicker cushion to sit on.
I personally prefer using LS motors set up this way, because it gives you more functional freeboard (the motor won't swamp if you come off step too quickly) and it is easier to drive standing up (great for jet boating and for driving through weeds/stumps, etc when you need to be able to see and pick your route).
Just my thoughts...