So from what I've heard, the 20" transom only makes sense if you already have a long shaft motor already. Otherwise, the motor sits a bit higher, sticks out more, and just is not needed. I saw pictures of one with a long shaft/20" transom and the top of the motor cowling was almost to the top of the flaps. So this is a con.
I believe all of my buddies with the old Duck Invader 13, which is the same boat, have the 15". I have the 15" as well.
The one thing I will say, used motors seem to be long shafts by a 2:1 ratio. Especially in the 25hp range. Reason being, a lot are sailboat kicker takeoffs or came off a high transom lake boat or jon boat. I went through a lot of listings trying to find a short shaft 25hp 2 stroke. That's the only pro.
If you are going to buy something like a new Yamaha or Mercury, just go with the 15" transom and order a short shaft. Much more compact setup. That's what I ended up doing. I have a 3 year old short shaft Yamaha 25hp on mine.
Boats are like nice firearms, more is never enough. 
I would like the 15" transom as well. I can't get past the part about them cutting 5" off the transom for an upcharge. Both the surgery and the fee are offensive to me.
