When choosing lighting fixtures for new construction, should I go integrated or non-integrated CFL?
While this is not really a diy type question, I'll give it a go.

First I take integrated as a screw-in self ballasted cfl and a non-integrated is a cfl with 2 or 4 pins made to go in a fixture designed for that lamp.

To answer your first question about new construction, some states have laws saying you have to use the fluorescent ballasted fixtures (for non-integrated cfls) in certain areas.  Residential it's in bathrooms and kitchens and outdoor lights.  I'm not certain about commercial buildings.  

All buildings, commercial and resi have to do load calcs (how much wattage a circuit will use).  While resi might not be as important to follow as strictly as commercial because of air conditioning impact and circuits will be more closer to the maximum output of what the wire and breaker are intended to handle.  If you use a recessed can that uses the integrated self ballasted cfls, or a can with a medium edison socket, then this throws all the calculations out the window.  

Put in a recessed can or fixture with a medium base, then building maintenance or Harry Homeowner will not care or know what was intended, they will put in the easiest to use.  In resi applications the biggest complaint I hear is when someone is putting on make-up, they would rather have the natural light of an incandescent than a cfl. Then 13 watt cfl becomes a 75 watt reflector lamp and the wattage went up 5 times plus the air conditioning burden just went up as well.  That's a big deal if done that way in a commercial building.

The ballasted fixtures using cfl's are limited on what can go in them.  Usually a 5 watt cfl has the same socket and ballast as a 7 and 9 watt.  A 13 watt does not share it's sockets or ballast with other fixtures.  4 pin tubes are the same.  That is why when it is governed that fluorescents must be used, they will only be accepted with no substitute.  Also fluorescent fixtures are designed to get the maximum light control and output of its lumens.

People that use the screw-in fluorescents use them for retrofitting from incandescent to fluorescent.  Probably the only advantage of using the screw-ins is that if the ballast goes bad it is part of the lamp, not a time consuming chore, depending where the ballast is.  Pricing varies but I would also suggest either trying another source for your lamps or bring in a competitive bid and have them start matching it.  Depending on how many buildings you take care and how many lamps you are responsible for, the big three (Sylvania, GE and Philips) loves working with people in your shoes.