Musician vs. audiophile

We need direction here. My wife, a musician and says my Sophia 3s, powered by BAT 3VK IX tube pre amp and 250w solid state amp sounds flat compared to a freaking Best Buy box store McIntosh/Martin Logan setup...  I can't honestly disagree, specifically when our rig is at low volume.  It lacks color and punch, even with 2ea. JL 12" subs... Help me with your recommendation, please!!!      
Musicians comprise a fairly large and diverse group of people and there will certainly be marked differences of their listening impressions. To suggest that not a single musician would find the Wilson good sounding is an obvious exaggeration to make a point. I’m sure somewhere a musician(s) is enjoying the Wilson speakers.
I would like the op to chime back in if possible with a bit more information like type and model of source, are the room sizes and types of the 2 different systems remotely comparable etc etc.
Having purchased the Martin Logan ESL from BestBuy, and having listened to all of the other box speakers there from B & W, Definitive Technology and Martin Logan themselves, and also having been listening to box speakers for 40 years by the likes of Advent, Genesis Physics, Infinity and Mission, I can state unequivocally that the ML's imaging, dynamics and tonality far exceed any produced by a driver in a box.  I totally get the OP's wife's opinion.

Do not know what your source is but it may be a little lacking or processed.  Some folks are beginning to recognize the musicality of well implemented non oversampling DACs - saying that even the best delta sigma dac implementation(s) sound less natural. Think Schitt
Yggdrasil, Audio GD-7, MDHT Pagoda, Denafrips Terminator, AMR 77 SE, etc.  Second I would look at tube amp(s) and/or upgrading your preamp to something like a deHavilland or Dan Sachs.  Finally, maybe what your wife is missing is something more dynamic and "wide open" - like open baffle speakers (Spatial Audio M3 Triode Master, GR-Research Super V), Magnepan, or even high efficiency horns. If you generally like the sound of the Wilsons, though, I would look at the source first, then the amplification. 

@uberwaltz touched on this but I didn't see it discussed in any of the previous posts (although I could have missed it).  It sounds like you heard the McIntosh/Martin Logan setup in the store - not in the same room as the BAT/Wilson system.  Could the problem be your room?