When I first got my MJ3, right out of the box it was a little bright for my taste (especially comparing it to my warmer Jot2). After 150+ hours of repeat playing on the amp, it started to mellow out and became smoother up top. Switching back to the Jot2, the Jot2 sounded slightly veiled in comparison because the MJ3 is so transparent and clean, that you see/hear a much cleaner window into the music. When I listen to the Jot2 now, I feel I am missing out on the finer details, not seeing/hearing the complete picture.
If anything, the MJ3 is very transparent where it will reveal bad recording (or upstream) flaws in the chain.
One thing I find when upgrading one component for another, its never always a one for one swap. Since the setup was built around an existing synergy, swapping out a component for another might require some minor tweaks to bring back that original synergy and to perform at its best. It depends how big of a tweak one has to do and whether the effort is worth it for them.