So it was such a huge success that they haven't made any other systemless settings?
I see it as entirely reasonable for Freeport to have been successful, but it not to be an easily reproducible success.
I think the biggest thing is that Freeport was an established brand, with a good-size fanbase, lots of previous books, etc.; it seems to me like doing a systemless book describing a setting with an existing fanbase would be less risky than a systemless book describing an entirely new setting. The other settings they published aren't so well-known, AFAIK. You couldn't remember the names of any of 'em, and neither could I -- I had to google to come up with Mindshadows.
The only other widely-recognized GR setting that I can think of is Freedom City, but there seems to be much less call for a systemless superhero setting. Most superhero games have their own settings, or just use a generic "today, with supers, like in Marvel/DC/etc" setting.
Also, the older versions of Freeport were long out of date, and for 3.0. Thus, an update was warranted when it came time to republish, and since GR had a few systems it could conceivably use (3.5, True20, wait for the upcoming 4e), a systemless book made sense. Freedom City is up to date with the current M&M system, so no updates are needed, and GR only has the one superhero system.
If GR wanted to license FC for other RPG versions, they could do that now, without the systemless book. I just don't think there's a big call for it -- Hero has a few Champions setting books, SW's super rules are tied up in a very specific setting/adventure path, and the other superhero RPGs are indie press books that use generic "just like your favorite comics" settings (and aren't likely to be huge sellers to boot).
Also, GR's spending their capital on other books (Song of Ice and Fire, Dragon Age, etc.) that they probably figure are better bets than Generic Setting That Even Internet Fans Can't Remember The Name Of.
That said, systemless books have historically, AFAIK, sold worse than non-systemless books. Which is fairly reasonable -- given the choice between Setting A, which is generic and systemless, and Setting B, which has stats for Your Favorite Game, I think most gamers will go for B, as it's easiest for them to use.