Many pros, and a few cons. The gist of it to fill you in...

Pros:
Brand new machine
Uses original Williams mechanical parts
No playfield QA issues of other manufacturers, including clearcoat problems
No original electronics including problems with those, such as GI diodes
Has been tested for years for accuracy and reliability, including in tournaments
Full support and warranty from CGC
Beaglebone Black CPU board and some RJ-45 cables are off the shelf
Uses less power

Cons:
Limited documentation on new electronics
Altered artwork to not include the Williams logos for licensing reasons
Some mods designed for the orignal game not compatible

I can't give you an exact list because I don't know what's out there, but things like electrical mods won't have the same circuits required to drive them. For example, an LED ColorDMD or various other things like LEDs that require specific playfield wiring and lamp sockets to work. Strictly cosmetic mods should be fine though.