So I've been thinking about this a bit lately. For starters, I enjoyed the film but that was mostly due to low expectations going into it. Reviews had been so harsh that I expected shit, and it was average. Very good visuals, sorta whatever story.
But I think it fell prey to trying to be 'too true to the source material'. Apparently Besson has wanted to make this movie since he was brand new and was a huge fan of the original source material which was a French comic strip that started back in the 60s I believe and has been running till near present day. So that is a lot of information and shit thats developed over the years thats totally not going to be able to be done in a 2 hr movie.
There are a lot of other things. I haven't read the comic, just read about it and supposedly Valerian was actually more a satire of the 'male hero man of action'. The original writer was apparently an old school feminist and made Valerian unlikable and had Laureline actually be the competent one with him being a jump in, punch shit in the face dude and she's actually the one that saves the day. According to wiki, it got so bad the writers realized that they had way overplayed their hand and had to redeem Valerian into being a decent character again. Now in a two hour film with the actor (who is in no way physically representative of that) it seems like they tried to do both. Make him a chauvinistic womanizing good guy and never really manage to develop it at all. He just kinda came off as a mess since they seemed to try and pack the whole 40+ years of his behaviour into two hours and its just lacking. One moment he's a heel, next they are trying to make him likeable and both the script and the actor don't seem to have the chops to pull it off. Top this off with how I feel in a lot of comics the characters are more a slow burn, minor developments happening around the story instead of it being character driven and you can see how they come off pretty flat. The movie can't decide if it should be about the characters or the story. Compare to Fifth Element were the story was pure who knows what the fuck drivel but the characters are very memorable and carry the whole thing. We all remember 'Multipass!" but sure as fuck don't remember what the fuck those stupid rocks were about.
Other main problem seems to be how 'episodic' and disjointed it seems. Its as if Besson took key little scenes from the comic's history and put them into the film. Where in a comic or graphic novel it might work cause you have a month or two between each 'scene' and so they don't need to necessarily flow into each other fluidly, in a film it just comes off as being a bunch of singular disjointed events. It seems like each scene was that month's graphic novel. The fishing for the squid thing. Last panel of the strip is her finding out where he is. Then next month is her finding him and then being captured. Then the red light district and rescue with Rihanna at the end is the following month, with them walking away hand in hand as the last panel of that month's novel. They all seem to be individual little stories with their own beginning, climax, and end that have an overarching background thread that ties them together, but really works poorly when you try and do it as a two hour continuous movie. It lacks the good overall narrative structure.
Basically, TL;DR. I think Besson is too big a fan of the source material and tried to be too true to the comics. A movie can't tell a story in the same manner as a once a month graphic novel, and he shoulda had someone else help him translate the novel into an actual movie script, and less a 'labour of love' to the comics.