I think on pure FPTP, smaller parties like the greens and Scottish Tories get ripped off in terms of Seats per Vote. At one point the Tartan Tories had 0 seats for their usual 20% of the vote. That's clearly not fair.
My main issue with the PR as per Scotland, is that you have MSPs who are not in any way accountable to the people. Anyone at the top of the Regional List is basically unsackable, as long as their party can get a small % of the vote in an entire region. I'm thinking Patrick Harvie, as one particularly odious and egregious example.