Chessbase once published an article that touches on this question.
Chess960 introduces very alien positions, such as this one.
[FEN "bnqrnbkr/p2p1ppp/1p2p3/8/2PN4/1P6/P3PPPP/BNQR1BKR w - - 0 1"]
Chessbase's comment on this is:
Here's another example: Svidler [Black] is still wondering, on move five, if he can move a pawn and not lose instantly, while Anand is pondering his 22nd move in a very interesting position. In the commentary booths, the GMs were discussing Anand's options with great excitement – he seemed to be struggling to equalize with white in a Sveshnikov! They were completely silent on the Aronian-Svidler game, as nobody had the faintest idea of what was going on. I think it was Tim Krabbé who compared commenting on a Fischer Random game to conducting a guided tour of an art gallery that you are visiting for the first time. Very apt.
Another problem with Chess960 is that some positions are more unbalanced than the traditional starting position. While some positions are also more equal, there are a few positions which start with more than twice the "normal" White advantage.
The final problem with Chess960 is that there's no continuity. If you play the opening position and lose to a spectacular new idea, you can study it back home, analyze where you went wrong, use the idea yourself, see if someone else can come up with an idea to beat this idea. In Chess960, nothing of this sort applies. Misjudge the opening and lose? Who cares, you're probably never getting the same opening again anyway.