JL Audio Fathom

Leave it alone. 

Two reasons, too many complaints about JL Audio reliability, as well as how hard it is to integrate a sub with main speakers.  If you have it dialed in don't touch it!! :D

If you want to really dive in though, consider a miniDSP along with the appropriate measurement gear to help you get to glory.

Also, room acoustics matter.  A reflective room, bad placement and big room modes should be dealt with.

No I would not switch. Doubtful the JL is much different from ML sound wise. I have had 5 (yes 5) failed JL E112s, friends don’t let friends by JL. 

I would not switch either. With the JL Audio you are paying a lot for room correction and a calibrated microphone. Room correction would be much better handled with a good DSP unit and REW.

I haven’t heard of the V2 JL fathoms having issues. The V1 definitely did. I haven’t heard the Martin Logan’s you have but can say the F113 is way better IMO to the Rythmic F12 I had. Much more articulation and punch.