The other thing about taking it to a shop, is in my experience they will never take the same time that you would to make everything absolutely perfect. Yes, the wires will be routed sensibly, and hidden but they won't necessarily be immaculately zip tied/techflex wrapped, etc because they probably didn't gut the entire interior to run them.
I remember a buddy of mine went to a shop to install his new Sti stereo, and he had all the components already including 100ft of new speaker wiring. Well they 'used' the new wire - up to the footwells, then cut the factory wiring and soldered the new wire there. The must have thought it was too hard to go into the door grommets
They also said his tweeters couldn't be used (they were too big to the stock locations) so they didn't install them. Uhhh... it's called a dremel, fiberglass....talent?
Of course there are some amazing shops out there that can and will do beautiful installs and flawless custom work. However - $$$$$$$$$$. You get what you pay for though. (Most of the time, sometimes you get ripped off when you spend a lot of money, but you'll never pay a shop $200 and get beautiful custom work.) If you do opt for a full custom install though, you'll be out your car several days anyways.
You can always post here any questions about removing/reinstalling pieces, you will get more than the help you need to do it