I've heard this problem repeatedly. I can give you my spin on it. In my experience, I never got the chance to go to design school. I was very technically savvy, which got me a gig setting up a print designers office about 6 years ago. He saw that I was intuitive and understood "complicated" things like layers in Photoshop or perhaps concatenating paths in Illustrator. However, I did not have good design sense. This working relationship has worked quite well. He has 30+ years of experience and knows how a design should look. However, he is dangerous on the Mac. He can't even figure out how to add a "no break" character to InDesign. Often times, bleeds are missing. Panatones colors are set used for 4 color jobs. I am the one who translates the design to the software.
You have your right brainers and left brainers. Finding one a student who can use both sides well is rare. We've had freelancers come to the shop with design skills and lofty ideas, how ever we wind up spending months teaching them how to mask, run filters, and name layers in Photoshop. Often times, simple skills like naming layers in Photoshop don't exist. InDesign files are a mess with dozens of phantom boxes and strokes. Files are placed haphazardly all over the server with what ever name the designer was thinking of.
I believe that we should teach more software skills along with a class of "naming files" and server organization. People who shoot out of design school are complete slobs. If they aren't neat and organized with file names and photoshop layers, it will cost your shop money cleaning up after them.
Many shops have the chain of command where the senior designer tells the junior designer what to do. The junior designer tells the production artist what to do and so on. The kid that comes in at ground level should be neat, clean and efficient with software. It's likely the designers above him/her already know what the design should look like. After years of direction, the entry designer will gain momentum and confidence working under experienced designers and move up the chain. He/She will find that their left brain will begin to work with the right allowing them to be creative and technically savvy at the same time.
This is again why I feel strongly about the CS suite. Learning software is very tough if you want to keep up with cutting edge design. Learning one Adobe product can be much easier once you've worked with another. Having to learn Quark, after working with Adobe Aps is like learning a second language. It may not take some people long to learn DTP's, but Photoshop and Illustrator can take years to perfect. It's not uncommon for my Photoshop files to have 100 layers after a couple of hours of instruction from the designer. He is finicky, and often wants to go back to a step from 1/2 hour ago. I have to be careful to build layers in such a way that I can find them quickly and bring them back up to edit. Some of our Illustrator work involves 5,000 sq. ft. mansions. The file is enormous, and I must keep it organized and easy to edit. If I'm not quick enough, the shop loses money. We've had "designers" come in to work on our files, and almost every time, a mess is made and the job takes twice as long due to poor software skills.