It's subjective. If you take, say, a Martin D28 (that has no pickup or electronics) and place a mic in front of it at a gig, this sounds completely different than an Ovation or some other Martin or Taylor that has an EQ and pickups built in running into an acoustic amp or through the PA.
General thought is that if you start chopping pieces of the wood out to install an EQ system, this will most certainly effect the guitar's tone. Whether or not you find this good or bad is up to you. I say experiment and try out different things and find something you enjoy.
I personally play an Ovation as my primary acoustic and have always enjoyed it. Opinions differ greatly.