It is all about the installer, but even if you have the best installer in the world and he is getting paid jack, then he most likely isn't going to do a great job.
I used to work at Best Buy, but not in car audio, I worked in the home theater installation dept. and it is the same, no pay=not the best work. I have my own company now doing both home and car audio and I work in multi-million dollar homes doing systems over $100,000 and I work on luxury cars such as Rolls-Royce, Bentley, Farrari, Lambos and more. My point is that it isn't the place, but it is how well the installer is treated, most of those people even jacking up your cars can do a good install, but they really don't care. Ask them to do it on the side and pay them, and I would bet they do a good job.
Best Buy does actually require MCEP training now for all installers. not that I'm saying that means anything, but how many of the custom shops really have training?