My feeling is that isomorphic instruments are ultimately superior, but the set of instruments used by professional musicians is pretty much fixed at this point (at least "classical" ones, because classical supposedly implies existing traditions).
A recent example (recent as in 1850s) of an "isomorphic <existing instrument>" would be a chromatic button accordion, eg here (specifically a bayan in this video):
https://youtube.com/watch?v=eDFFUIGoBUc
I feel like the callibre of music played on CBAs is much higher than on diatonic- or piano-accordions. I kind of wish an isomorphic version of a piano had become the main form of that instrument somewhere in the world (as the bayan did for accordions in Russia), since I feel like it might have similarly improved on what music is playable.
On a related note (hehehe), I posted this comment recently about my own use of the isomorphic layout used on bayans (including a video) .. though I'm not a trained musician:
You lose some idiomatic guitar vocabulary, but if you don't care about that you gain the ability to construct your own chord voicings much more easily, and only need to remember one fingering for each chord instead of three.