Upgrading from Wilson Sophia 2's?

What is your budget?

Without knowing that, it is difficult to give you a good informed answer, but, off the top of my head, I'd say try something from Sonus Faber or Avalon Acoustics. Both of them make some of the most non-fatiguing speaker that I know of, and yet are very high quality.

By the way, do you really want to upgrade as the title of your thread suggests, (i.e. do you wish to spend more money than the Sophia 2's cost?),
Or,
Do you just want to swap them out for something in the same ballpark?

Good Luck!

PS It might also help to know where you live, so that we don't suggest something that is not available in your area/country.

Verity Audio Parsifal Encore or ovation. I have spent time in the dealers with the Wilson's, I think I know what you mean, they seemed a little forward in the upper mids, lower treble, (thought room set up and tastes can make them perfect). I have been stunded by my Parsifal's and will keep the speakers as I upgrade everything else along the way. A more refined, subtle presentation that does not grab you but quietly seduces you.

I would look at room treatments if you haven't already done so. I was having a similar problem with my Mini Utopias, too bright and aggressive on so- so recordings and some panels from Ready Acoustics helped quite a bit. But there seems to be a tendency with Focal, Wilson, and some of the other high end speakers to go for the last bit of detail. I spend most of my time with my Spendor SP-1/2e's, which give a more relaxed presentation. I have also read good things about S-F but no dealers near. I would check out the room before I did anything else. Mine is 13x 35 and I found I was getting good response at 32Hz, way down at 50 and 62 and back up at 100. [I use 2 REL Stadium Subs]. This made the sound more aggressive than it is after I put up the panels. Response is now flatter and sound fuller. Hope this is some help.

Do you experience this with both your analog and digital front end? I bet the Sophias sound excellent w/ good recordings (as mine do). If your goal is to set-up a system to make these inferior recordings sound "good", I fear you will end up with a highly colored system. I would experiment with speaker and listening chair positions, room treatments, and cables before giving up on the Wilson's.