Sgt_Kickaxe - 4:02 am on Nov 10, 2012 (gmt 0)
If your site uses extensive redirects, as many affiliate sites do, the number of "not selected" urls can be high naturally. Robots.txt files do nothing to help that and a noindex meta tag on the redirect page is of no help since it won't be read.
I'd be interested to hear how you redirect your links to an affiliate site if GWT is NOT reporting a high number of unchosen urls.
Otherwise I wouldn't worry about it.