3D ones look slightly more realistic, but when retracted, the doors don't blend in with the fuselage, and stick out like the dog's proverbials:

Fake/flat ones don't allow you to see the gear inside the bay, but they use slightly less poly's and allow the fuselage to look nice and smooth when retracted:

Not evident here because I haven't mapped them yet, but on the "fake" version, the gear doors and all details on them will still be visible when retracted.
Here's a better view of how the 3D ones look when retracted:

Fake:

PS... my first attempt at a poll, hope it works right!