I am probably biased as I currently work for what might be considered a regional "boutique" or "specialty" integrator with two branches and a 25-employee highly qualified staff that focuses on larger municipal projects. I have also worked for a large national integrator in the past.
Yes, I think the regional "boutiques" have advantages over the large national multi-branch integrators mentioned. We routinely do larger instllation projects at local airports, courthouses, and universities, so don't let size fool you. However, large national accounts such as chain stores or corporate offices will likely never be installed or serviced by local integrators as they can't cover as much territory as the nationals, so they do have an advantage there.
With just about everything connected to a CAT6 cable now, the number of installers needed for a larger video system has dropped significantly. Many times on a new project, the structured cabling contractor pulls the network cabling for the cameras, so installation becomes a matter of hanging, aiming, and focusing cameras and an having experienced field engineer to do the head-end software setup and configuration as well as coordinating the network requirements with the customer's IT staff. The size of the installation departmetn doesn't matter as much as it did back in the analog days.
Many times a large local customer prefers a regional "boutique" over a national as they may have had difficulty in the past getting resolution to lingering issues or personalized service from the national and they have more influence over a smaller regional or local single office integrator. We have several major accounts we have taken over from the national integrators due to price, the proprietary nature of their systems, poor service or the the hassle of dealing with their salespeople or corporate policies.
In my opinion, the national integrators try to "be all things to all people" with average product offerings service (been there, done that). It is hard, if not impossible, for their service techncians to be competent in everything they sell. The best analogy I can use is you know pretty much what you will get when you go to an Olive Garden or Chili's restaurant anywhere in the country: consitently average food with identical menus and portions. You won't be totally disaapointed but you likely won't leave going "Wow that was a great meal and the service was fantastic". The "boutiques" have a niche market or specialize in just a few VMS's or brands of equipment and do them very well and have the flexibility to offer service plans tailored to the customers needs instead of a one size fits all solution. To continue the analogy, think of them as the regional chain or local restaurant specializing in a single type of cusine with good food and personalized service, but you can't get it anywhere you go.
One thing that does bother me: I have seen many times where a project is specified for a partiuclar VMS or system (especailly ones we help specify) that a few national integrator's local offices respond to the bid invitation even though nobody from their local branch is certified and that branch has never installed one before. Another branch in a different part of the country did one in the past, so they have access to the software or the equipment from the manufacturer. Caveat Emptor! End users, before you sign that proposal or contract from a national integrator, make sure the LOCAL branch technicians are certified on a product and have experience with installing and servicing the systems.