I don't really have that much issue with her voice sounding different since the Usagi of Crysternal and the Usagi of the '90s anime are different characters...
What's more jarring is that it's clear that the others voice actors are not really contemporary to Kotono or really her peers in the same sense that the original voice actors for Mercury, Mars, Jupiter and Venus were. It kind of exasperates the distance between Usagi and the Inners which was already a problem in the manga, but seemingly more apparent in Crysternal.
In that sense, I completley agree that they either should have kept as much of the original cast as possible or recast everyone. Or if they were going to recast everyone but Usagi, hire voice actors that are closer in age to Kotono so the age gap just doesn't feel as apparent.