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!!!      
repeter
If you do not like the sound of McIntosh and Martin Logan then you are in the minority.  I loved them when hearing a demo.  As a musician your wife has tuned ears.  I am the same.  Not only the music but the accuracy of instruments sounding as live.  Violin cat gut vibrating cello string.  Can you hear the resonation of the wood chaber of the instrument.  Other people listen differently.  I thought a pair of B & W 683s I heard at best buy were harsh in the highs and had no dynamics in the bass.  Could be the recording?  The demo room?  Many people like them but I did not.  So I fall in your catagoy there.
trelja, I couldn’t agree more.  Love the ESL57’s for their amazing midrange purity.  I don’t own Quads, but that level of midrange and high frequency correctness is the reason that I put up with my Stax ESL F-81’s maddening low end and SPL limitations; amazingly realistic timbre which rivals the Quads, imo.  Driven by tube mono’s in many respects they make some of the most realistic sounds I’ve ever heard from a sound system.  
I agree with Stevecham. If you are using subs they need to be timed correctly with your mains. Most mains react a fraction of a second faster. than the subs. Use a processor or cable lenth to correct this problem. When you got it right your bass will pop. I have a 4 millisecond delay to my mains in my system. Bestbuy in my city has a Magnolia store inside select Bestbuy that is separate operation that carry high end equipment.
I'm a life-long active musician - big band swing trumpet player:

http://hornsaplenty.org/

My wife is a professional classical violinist

http://temescalquartet.com/

We've both acoustic musicians and so we mostly listen to acoustic music and have a preference for real instruments to sound like themselves.  If I were you, I'd use acoustic instruments as a reference.

What finally brought our system fully together was adding in a miniDSP DDRC24 active crossover and DSP EQ.  After measuring the room and impulse response with the included DIRAC software, I set the target response to the Harman EQ curve.  That brought it all together and gave the system that final bit of true naturalness.  It took just the right amount of edge off the violin upper register and evened out the low end.

I don't know any of your gear, but you should expect a Best Buy demo system to be tweaked in such a way that it makes you go "Wow" without actually being a natural presentation.  Remember that stores like Best Buy sell the sizzle, not the steak.