I think manga is and always will be better.
My reasoning is as follows: manga allows for more expansion on storyline, since Its not limited by the screen format. There are just somethings that can be done in Manga that can't be done in animation.
There are also instances where not all the story can covered in the animated series. One prime example of this is Kare Kano. The manga is 21 volumes. The Anime series is 26 episodes, but only covers the first SEVEN volumes of material.
There are also instances where the end of a series is a cliffhanger, a good example of this is Ai Yori Aioshi.
I love animation, always will, but I get more enjoyment out of reading something. Like Tsu said, you actively participate in the experience. Your brain has to work to fill in the blanks.
In animation, everything is done for you. Sure the story's great, its animated, in color, there's voice actors. But you're just a Lazy spectator.