Option two is a lot of hassle and you've already described the downside yourself.
Option 3 will make it difficult to sort through your members by skill as mysql won't sort through the arrays in each record (well not that I know of anyway - if someone cares to correct me I'll be glad to learn as I could use this myself!).
Option one from my POV is the only way of doing it.
PS my comment was a joke.. I simply didn't reply to your question because I had square eyes at the time and couldn't really understand it lol (that'll teach me for staying up late again lol)
My helpful sig has gone because a mod below the administrator gave me an infraction - despite the administrator personally agreeing to it.
If you need any php tips or tricks you can PM me.