In a fantasy world where I somehow had the ability to design the layout of St. Pancras...
Divide the main station roughly in half, split between Eurostar and MML (which would have full-length platforms within the trainshed). Build additional platforms (for HS1 domestic) in the undercroft. It should have been possible (with some engineering effort) to arrange it such that the upper and lower HS1 tracks run alternately, with the upper level platforms covering the lower level tracks, the real-life arrangement of tracks appears to have more than enough space. The "ramps" would take space away from the lower level platforms, of course, but that's OK since HS1 domestic trains are shorter than Eurostars. Put the Eurostar departure lounge, customs, etc. in either the Hotel building or the buildings on the western side, with access to the platform via bridges, similar to Paris Nord. Eurostar arrivals customs could either be in a small structure at the London end of the platforms or in the structure along the eastern side.
That arrangement would allow a full-width concourse (since Eurostar would not be accessible directly from the concourse) used only for MML passengers roughly on the same site as the station's original concourse. Since the lower level (HS1 domestic) platforms would only take up half the width of the undercroft, there would still be space for an access route to Thameslink and retail spaces, albeit without so much natural light.
Also, a direct underground connection between the Thameslink platforms and the Underground (the northern ticket hall can't be that far from the Thameslink platforms; there's no need for easy access to the Circle/H&C/Met since Farringdon exists) would reduce the amount of foot traffic through the mainline station.