Unless this is intended to be a short mini-campaign, do NOT use the permanent damage table. PCs generally become the walking wounded in short order, and nothing ruins a campaign like players unhappy about their characters.
I think most of the others are fairly reasonable. I don't use the mark option or flanking, but that's personal preference. Marks are hard to keep track of, and flanking generally creates conga line combats (as it did in 3E and 4E). I have my own house-rule on healing, so I don't use either of those variants either.