I've owned both a PA 12 and a PA 18, though my PA 12 was mostly stock.
The big difference in the two airplanes is width of fuselage at the "waist" and the angle of incidence of the wing. The 12 has a different angle of incidence, and unless you mess with that, you'll never QUITE perform with a Super Cub, even with flaps, same HP, etc, etc, etc.
And, there are a LOT of etc's to make a 12 even close to an 18. The gear is different, and the 18 gear is much more robust, for example. The 12 did not have aerodynamically balanced elevators, the 18 does, etc, etc.
One advantage the 12 has is better ailerons, though.
A highly modified 12 is a great airplane. Then again, so is the 18. One other advantage of the 18 is that you can legally increase the Gross Weight to 2000 pounds with a Wipaire stc. The 12 can go to 1935 on floats, but I don't think that applies to wheels, and 12's tend to be heavier than 18s.
Either one is a great airplane, without doubt.
One more thing: a lot of folks buy a 12 based on the fact that the back seat is certified for two people, so it's a three seat airplane. First, double check the weights, as noted above. Second, try fitting two "normal" size people in that back seat, and then keep them there for more than a half hour or so.....you may convince them that they never want to fly with you again.
Good luck in your search. There are some great 12's and some great 18s out there nowadays.
MTV