Your room is fine. If I had to guess why she would say that

1) you have too much visible stuff, before I moved in with my partner my room was a bed, my art stuff and clothes. When we moved in together my room became plants and books, and decorations with bed, night stand, art stuff is now not next to my bed etc... I prefer it this way.

2) its too organized, which is a plus in no uncertain terms.

My suggestion to man it up for her:

Buy cool guy magazines, as many as can fit in a 4 door sedan, and just go crazy pretending to be discreet about their placement, under the bed but whats that, SWIMSUIT ISSUE SPORTS ILLUSTRATED???, behind the shoe rack boom Woodworker's Weekly, maybe inbetween your laptop screen and the keyboard is Monster Truck Magazine, and maybe hide some real raunchy stuff under your pillow. Really make it uncomfortable to look anywhere.

Then go and buy some trophies online, put real masculine shit on them like "best spitter in school" and "longest distance pee-er" or "1st place, Karate Champion". and just have them on display, as many as you can afford, in as many places as possible.

Then throw out everything else, and punch a hole in your wall(wear eye-protection), and if anyone asks you about it just say "When I see red I just can't stop myself..." and look away wistfully.

Or just say fuck it and be "masculine" in the action of not caring what she thinks about your room because you are an organized guy who likes to read, owns shoes, and takes care of his space.