- it's less expensive, overall
- smaller total footprint
- fewer items connected to the APM2 that might carry vibrations to the accelerometers
- Can position the GPS more flexibly, get it away from local sources of RF, magnetic fields, speeding up 3dfix times
- Can (easily) upgrade the GPS to a battery backed model easier
- Can (easily) upgrade to a higher quality GPS with specific features you might require, high altitude, more precise
- Can position the GPS in a place on your airframe that is easier to see the 3Dfix LED (which does not confirm that the APM2 has a fix, but so long as the cable is good, a solid 3DFix LED on the GPS model usually means a 3DFix for the APM2.
However, you can have the best of both, if you want. We have figured out one of several ways to get an APM2 with an onboard GPS to accept an external GPS. See Colin's solution at the bottom of http://diydrones.com/forum/topics/jumper-s-for-apm2-onboard-gps
Other than what has already been written the APM2 Shield GPS antenna will detach in a crash.
Always go modular whenever you can. 99% of the time modular is the correct design choice.
Just read all the posts here where people are having trouble with the GPS, or for whatever reason want to connect an external one. The internal unit highly limits your choices unless you like cutting PCB traces and/or SMT soldering.
My gripe with the APM2 design is that you can't mount it for proper GPS reception. Because all the wires and connectors come straight up you can never get a 180 deg. clear view of the sky. Your APM/GPS is always buried in the plane and it's also buried under a bunch of wires.
I should probably also point out that despite the IMHO sub-optimal positioning of the integrated GPS in the APM2... I have never had a problem with it. My GPS locks fairly quickly and I get better than 3 meter position fixes 90% of the time. All of this inside a foam plane, under the wing, with wires running around haphazardly.
In my open air tests (outside the plane) walking down a sidewalk it tracks me usually right on the sidewalk and occasionally jumps out to the middle of the closest road lane. Usually that happens when walking under trees or near buildings.