I don't understand enough of how you see things to say whether it's right or wrong, but if you're saying that the fact that so much of universe is plasma is unintuitive because so little of what we contact in daily life is plasma, then I certainly agree.
I dont' mean that its unintuitive because of what we see in our daily life (well, it is, but that's not the point I was making). I see saying "99% of the universe is plasma" as analogous to saying that "99% of our solar system is the sun".... Sure, 99% of the mass of the solar system is the sun, but that doesn't paint the right picture of what the rest of the solar system looks like, which is very non-sun like.
Typically, when people picture plasma, they think of hot gas. So when someone hear's that 99% of the universe is plasma, I don't think that paints the picture of what is really happening in the interstellar regions of outer space. Sure, it technically counts as a plasma, but since the density is so low its not really what people are thinking when they picture it.
I think that's part of the point of saying it that way. Its supposed to be a "wowzer". The physics cranks seem to like to say things that appear false at face value, but tend to be technically correct. That way, they can build some doubt as if everything you think you know could be wrong, and therefore, all of physics could be wrong too. I don't find it to be a very honest approach.