Interesting. So you're saying the 1/4" plug out of the guitar to an XLR on the other end to input into the amp, and that will make a marked difference in sound?
Well hold on for a moment...yes and no.
Your initial post was with regard to your ES (which BTW in 2012 was the ES 1, but the third update, which many abbreviate as ES 1.3). It is a very good sounding system,
but assuming it is in proper order, if its tone is not to your liking, then it likely never will be. Some folks simply prefer the piezo tone, as this is what is commonly used in a bazillion guitars out there (like Taks and Martins). So if this is what one is accustomed to hearing, then the ES 1.3 can put you off ...again, assuming your ES is good and not faulty.
The balanced cable (1/4" TRS to XLR) does
nothing for tone, nothing! Running a balanced line will give you a stronger output (6db, IIRC), better signal/noise, and eliminates issues when cable-length is long. If you have no issue with getting proper gain and have no cable-noise issues, then using a balanced line does
not improve anything.
I would go to a store and compare your guitar with another ES 1 guitar off their wall and see if yours is, indeed, working properly. From this point, you can then decide which direction to go.
And as for the "mic" input on your Fishman, I will "guess" that they EQ'd that preamp for vocals, so plugging in an instrument may not get you the best results. But that question is best answered by Fishman ...drop em a line and find out for certain. Hope that gives you a few things to think about.
Edward
