You should make an informed decision!!
From an electrical circuits standpoint, shorter leads are better -- they waste less power, and they present a nicer load to the ESC the shorter they are. But shortening them presents the obvious problems:
- You lose "meat" that you can use to fix problems short of tearing things apart and replacing leads or rewinding motors
- You may not be as good an electronics technician as "they" have at the factory -- 'civilians' can so screw up a simple soldering job, I'm not surprised that E-flight would try to keep anyone from trying
- You lose mechanical isolation between motor and ESC -- meaning that it's harder to dress the leads for low stress, that there's going to be more vibration transmitted from motor to leads leading to faster wear on the connectors, and there's potentially a bigger chance of the leads getting yanked out by the roots in a crash
From an electrical standpoint, unless the ESC circuitry is really weird, the best connection would be the shortest possible leads from ESC to motor, with no connectors at all. From a mechanical standpoint, however, you want to have a service loop somewhere in the wiring harness to mechanically isolate the ESC and motor, and just for convenience sake you want to have connectors in there.
I'm a fairly good electronics technician (I'd say this was because I'm an electronics engineer, but any full-time technician would laugh me out of the room if I did -- it's because I had experience and training as a technician before I got my engineering degree). So if it looked easy enough to replace the wires on the ESC I'd shorten them as much as possible, and put connectors on them at the ESC side. If I thought it was worth it I'd go ahead and void the motor warantee, but keep in mind you want at least
some slack, and you probably want enough for a small loop in the wire, or at least a pronounced 'U' bend. If I were doing some special-purpose, super-zoot plane (like speed) I'd strip the cover off the ESC right then and solder the motor wires straight to the pads on the ESC -- but that's a bit crazy for a control line stunt plane.