And whats the deal about Ryouko being 2000 years old and Washu
being traped for 5000 years?

Umm... there's another problem here... according to Mihoshi's 
ship AI, Yukinojo, Kagato is 5000 years old.

Hmm... Could Kagato have been the physical incarnation of 
Washu's own dark side? Something that manifested itself somehow 
and then imprisoned her?