Did you watch the extended cut? I always thought the added scenes helped make sense to some of the plot parts and just to the characters in general.
There is also a long version of the film, referred to as "international version" or "version intégrale". Containing 25 minutes of additional footage, it is sometimes called the "Director's Cut" but Besson refers to the original version as the Director's Cut and the new version as "The Long Version".