Yes.
He was a legit genius, and it comes through in the sit-down interviews he did, especially later in life. Whether you like him or not depends on what he was using his genius on at the time. Sometimes it's freakout edgy songs, sometimes it's composing modern classical music, sometimes it's wildly complicated instrumental grooves that hasn't been matched since.
I think the common dissonance people have when exploring Zappa is the clash between the music and the lyrics. You'll be listening to something zany and interesting, and suddenly Zappa breaks in talking about banging hairy girls, or going blind from eating yellow snow. Even the instrumentals are jarring, you can listen to a 4 minute groove that seems to be building to something, and suddenly it cuts off cold with a 5 second xylophone solo for an outro.
I can't say those choices are bad, and others claim to get it better than me. But even if they're pure genius, they aren't able to be conventionally packaged or appreciated.