I love the wall colour it looks nice teamed with the timber. Could you perhaps remove the mirror on the dresser it would immediately make the room look less cluttered. I love that train picture and think it would look great above the dresser on the wall? I am a big fan of toy hammocks (check out the one in my sons space to create some storage up high. A toy box / bench seat for under the window would give you heaps more storage than the current toy caddy. The room doesn't feel dark though I realise pictures can be deceiving.

i don't think it's dark at all. it's totally normal for a young boys room to be messy. As far as the closet goes I would by the rolling stacked storage drawers at walmart or even tubs. why/what is that extra piece of furniture in closet? get rid of it and use that space for shoe organizer or something more useful. Get rid of the large lamp on dresser. Boys don't care about big mirrors either. Try different furniture arrangements & donate all the un-used stuffed animals to a kids shelter. Get rid of the high shelf at top bunk with all the junk. get some sort of arrangement of what you do have on the walls it's so just thrown around.