Basically, you're asking about choosing between the two for merits, right?
Um... I want to say that GAxe is going to beat dual axes by around 17%, assuming **** near top-of-the-line gear in both setups, but I'm seriously half-assing the numbers for that calculation for assorted reasons (mostly "they're kind of a pain in the neck to do in full and taking everything into account" - last time I did an in-depth comparison of anything, it ran to about four posts landing right around the 100k limit apiece).
Figure on it being closer to 5-8% for the amount GAxe is ahead of dual axes by, in general. The main advantage of dual axes is in any situation where you have a SCH/RDM for Enspells on everyone and are getting at least double March - and then it's just that you're getting that additional ~16 damage about twice as often as if you were using a GAxe. On the plus side, it's not normally that far behind, either, outside of WSes (two axes' combined base damage is going to be right around the same as one GAxe's base damage, and you then get to count fSTR twice in there, so one attack round is going to be pretty close to the same damage).
SUPER BANNED FOR FAILING TO POST 20K IN A TIMELY MANNER