Weekends at Tokyo Disney are insane year round. Weekdays are crowded as well, but not usually as bad. Next time be sure to go on a weekday, and regardless of what day you go, if you don't arrive before park opening you're already hopelessly behind for the day.
Don't miss Sindbad's Storybook Voyage (grab a Chandu tail next door!), Tower of Terror and Indy in TDS. Toy Story Mania is an exact clone, skip it. Big Band Beat is amazing. The Mermaid Lagoon Theater is fantastic and offers Fastpass. Journey and 20K are very much worth doing, if a little frustrating in their execution.