We actually went through this last year.
Oracle, one of the major sponsors of our school and team
is building us a brand-new facility on their campus in Redwood Shores, CA. We actually broke ground a few weeks ago.
I was on the student/staff/parent design team for it and was involved the most in the design of our shop, so I know a bit about that. In general, what everyone has said is great. Make sure you have drops for air, power and data above all of the different tables/work-spaces you might have. If you aren't sure if a particular drop will be used, include it anyway. It's going to be a lot harder to go back and add things than just including it as a precaution. The same goes for things like ventilation and fume collection. Even if you don't do welding now, it's going to be really expensive and time consuming to add that later. Another local team had to do that and it was a total nightmare. Wire up large outlets (Single and 3 phase) for big machinery. Like others have said, make sure you have a way to get things in such as double doors or a roll-up door.
The shop at the new school is two floors. The bottom is where the wood shop and metal shop will be. In those rooms is all of the assorted machinery and tools and workbenches. There is an office for our shop teacher and a fairly large materials and project storage room attached. Upstairs is a design studio, with 3D printers, laser cutters, etc. and computers with CAD and design software. There are also lots of large tables for group collaboration.
I hope all that was helpful. PM or post if you have any questions!
__________________

2016:
Team 5940 (Silicon Valley Regional Rookie All-Star and Quarterfinalist, Curie Quarterfinalist)
Volunteer: 2016 (Chezy Champs Field Reset, Capital City Classic FTA, MadTown ThrowDown FTA)