Great idea! If you do some simple rewiring this can work facing any direction. So if you are having trouble with your center pistons not working properly try to follow my redstone diagram below and it should fix the problem. Note that the different colors represent different height levels. Use the profile view to figure them out.
I feel kinda really really stupid right about now.
I made one of these piston docks about two months ago, and joined them together to make an awesome dock but I never got around to posting it. It's much more compact, and although it's much deeper than his, my version can be positioned directly adjacent to each other, and if you want, back to back. (see picture) It doesn't use pressure plates, but I wired some up in like 30 seconds, and they worked just fine.
Here's a picture of what mine looks like. (The redstone for the piston dock only goes two blocks past the raised part of the dock.)
Our designs are pretty similar, but it's a lot more complex on the circuity end. It's wired up to a lever, instead of a button. The signal runs through a limiter, to make sure the pistons don't stay down; and then a monostable circuit, to make sure they stay down long enough to let the boat in. I would have preferred a button, but I couldn't keep the water out of the redstone connecting to the button unless I exposed redstone to the surface. I had kinda dismissed the pressure plates for aesthetic reasons, but they actually work much better than the lever. I actually made two working designs. One uses a pulse limiter + monostable circuit, and the other uses a RS NOR latch wired up to a ton of repeaters. (Pictures from the front are here and here, respectively.) They're both wired up to a lever, but it can be changed out for a few pressure plates. As a note, I used one row of repeaters to power the pistons, instead of using two different sides. I just fed the signal upwards using torches. It was much less messy to wire, and the extra depth gave me room to squeeze in something to extend the signal to make sure the boat gets all the way in the dock.
If anyone wants an Mcedit schematic, I might grab it and post it, but I'm kinda bummed that someone got a digital diamond for this. I didn't think it was that special.