Just to clarify, you're saying you recorded your Martin with two mics; then recorded an acoustic via its built-in pickup? Via a jack lead?

Personally, I hate the sound of an acoustic guitar recorded via a pickup and jack lead. It's mics and nothing but for me, every time. I'd really like to hear those recordings, because I pride myself on always being able to tell the difference between a jack-lead-recorded electroacoustic and an acoustic recorded with mics. The former always sounds really plastic and lacking in warmth and body.

I'm not irredeemably an audiophile snob - I often prefer the sound of cheap guitars recorded on cheap microphones, and I actually like a bit of hiss in the background - but I can't help but suspect that if you're not hearing any real difference it's cos you're not using a decent condenser (or ribbon) mic.