I've read the film novelization. The lack of story behind the game is purely a game choice, trust me on that. In the film Qwark is never a bad guy, he's tricked into siding with them because he's an idiot, for example. Most of the new characters are fleshed out, there's a hint at Clank's backstory, and so on.
The game seems to have been held back in the plot department because of the film, nothing more. The film is supplementary material to the game, required s bit for the plot to start coming together in any meaningful way. Otherwise things just happen.
You should check out my YouTube channel, The Golden Bolt! I review all types of video games, both classic and modern, and I also give short flyover reviews of the free games each month on PlayStation Plus to tell you if they're worth downloading. After all, the games may be free, but your time is valuable!
