: They look short and fat. What is wrong with them?
Well, nothing is "wrong" with them as long as you buy or build a boat that suits your needs. I've got a friend who has a 12' or 13' Wilderness Systems Pungo. He takes a six pack and his Golden retriever out in it on calm Sunday afternoons. I've paddled it and it's great for what I just described, but a total pig for any sort of longer distance paddling or rough water and wind. It's really a leisure boat that's great for fishing or relaxing in protected water. Long distance overnight touring? I wouldn't consider it.

:Can I take a longer design and just compress it a little to fit my storage needs?:
It's not that simple. Most kayak plans are designed for a particular displacement (performance at loaded weight). Just shortening the plans could cause all kinds of handling and displacement problems. OneOceanKayaks.com does a great job explaing what that's all about...

: Do the commercial guys not care about what they sell or are the strip designers only publishing almost perfect plans and not bothering with plans which have many shortcomings?

If you've been in a bicycle shop, you've noticed the high end and high dollar road bikes and mtn. bikes as well as the heavy and slow recreational bikes. Each has their place and kayak companies are very similiar. The problem comes when they sell you a 13' Pungo to go paddling with all of your friends who happen to be paddling 17' Arctic Hawks. Like putting a Yugo with a gang of Saab Turbos.

A couple of designs immediately come to mind for the kind of paddling you're describing. The CLC Mill Creeks are stitch and glue but can be built with a strip deck and they're probably perfect for what you're describing. A few builders on this board have done that and they're REALLY beautiful boats. Do you have much work space?
I just finished a Caspian Sea stripper by John Winter that I call the Dragonfly. It could also fit your requirements but would also be suited for open water and chop. I'm 6'1" and 220lbs.

I also built a Storm by OneOceanKayaks that is more of a performance boat. I think of the Caspian Sea more as a really nice high end mtn. bike and the Storm as a very refined road-racing bike.
You can compare the two, the Storm is at:
www.kozelguitars.com/Storm/frameset.htm and the Dragonfly is at www.kozelguitars.com/dragonfly
You can see that the boats are quite different.

Well, anyway, you already know the kind of paddling you want to do. Now it's just a matter of finding the right design to build. I've just suggested a couple and I'm sure there are a number of designs others will suggest.
I've attached a picture of the Mill Creek from www.clcboats.com