Given that he had just one on-screen appearance in the Doctor Who franchise I'm not that shocked that Paul McGann doesn't get a lot of merchandise, but you'd think that---if for no other reason than to have a complete set of figures representing the entire Time Lord saga---they'd have a couple of them floating around.
Yeah. The box set is currently the only way (other than eBay) to get all eleven Doctors.
It's like a line of Star Trek figures without at the very least a couple of Jeffrey Hunters being in circulation somewhere.
Kind of like the original Mego line (which I did have as a kid).
Speaking of Trek toys, a dream I had was for a 3.75-inch line that ran the whole spectrum, from TOS to Star Trek XII (with a line of ships, phasers, etc., to match). But I think the reality of the current toy industry--in particular, action figures--makes that idea unrealistic, especially with Hasbro now having the license (perhaps they'll let another company have a sub-license for that--hopefully).
One thing I've been seeing Hasbro and Mattel moving towards is releasing figures solely through subscription clubs, which is essentially the same as making them rare (i.e., expensive) online exclusives.