I must decalre an interest as I'm a serial ACG abuser.
To my mind it's an upgrade / update on the classic (in my case Fender basses). I think the core designs Leo produced were groundbreaking but not perfect and I personally don't have a problem with innovation and improvement. I'm sure with the right wood choices etc you could get the exact same sound if that was the goal. For me the most disappointing thing about Fender is the lack of development / R&D. It just seems like a load of re-issues coming out and escalating prices to accompany them (you'd think they that would have cracked how to make them by now).
One issue with custom basses I think is the resale value were you to move them on. They are by their nature personal things and thus a buyer might be harder to find. If you're buying a 'preloved' Fender J or P you pretty know what you're getting and I think second hand values reflect this. Not an issue for me as mine will not be for sale!
It is a very personal thing and probably divide opinions in a marmite type way. I have owned an MIJ Jazz (fretless) and an MIM P and tried a couple of MIA Fenders, but imho the fit and finish on the luthier made basses leaves them for dead. The weight and balance is considerably better too.
The Graft bass spec would provide a person with a hand crafted bass with more love and attention to detail than Fender US have the time to languish on their output, for less than £900. I am picking up what is essentially a J bass tomorrow (the neck p/up is a single coil) except for the overwound bridge p/up and a slightly different control setup of volume / tone / pickup selector.
http://www.acguitars.co.uk/acg_admin/wordpress/portfolio/2881/
I am also fortunate enough to own a full custom spec J type fretless which cost a good chunk less than £2k and is outstanding in every possible way (imho of course ).
http://www.acguitars.co.uk/acg_admin/wordpress/portfolio/0120-custom-j-type-fretless-4-string/