seems like the inverted fork would get more dirt and debris on the seals. thats probably not a problem with the technology these days, man has conquered small debris particles.
a buddy of mine who is a motocross rider said that inverted forks are much stronger than conventional designs.
i however do not think we are in the infancy of suspension. its all relative though.
http://www.mombat.org/Suspension_Museum.htm check out these dinosaurs.
:edit:
http://mombat.org/Suspension.htm