Try This? Visual Illusions.
I can see the actual size of the ad is reduced but the boxes surrounding it makes up "blank" space. It makes it an optical illusion that the ads are "bigger" when if fact it's the empty space of the template that's making everything smaller. Removing the template all together and just having thin lined borders in your color scheme "could" eliminate this visual problem.
If you get rid of the light blue background and expand, then you would be solving a lot of the "squished" illusion people are seeing. The blue surrounding the white by terms of what the mind reads is "cold" the light blues are in fact, making the white stand out. The eye has to adjust from the light blue, to the white, then read in black. Whereas if you had blue and a white text background...you have to have a similar color text in blue. But colored text IS hard for some people to read. On your current format, the eye is getting tricked into thinking the black is "gray" because of the light blue surrounding.
This is why it appears messy is because of the "afterimage" illusion. Every time you make a different theme to the website, you have to do visual illusion tests. Read a little bit, scan over the whole page...then close your eyes or look towards a blank wall. If you see too many colors and blocks burned into it then you have a messy format.
If you need the colors to be eliminated for readability then you must also remove the "theme" colors surrounding the text on the left and right. Which means only the silvery gray blue colored banners should be on the tops and bottoms of stories. With a complete white background where the stories are written. Boxes should be defined by lines instead of blocks. Also to completely maximize the story section, have the user avatar, information/tool box going directly above or below the story content. What you have is a very horizontal scheme. Web pages are by "nature" vertical. You're creating a horizon where there needs to be height, not width. All of your options are getting squished side by side on the page. It should be one on top of the other for more visual focus. The comments section should not be wider than the stories themselves. This would be fixed if you do move the left side bar towards the top or bottom of the story and widen the story to take up the sidebar/"tools" place.
For example...check the editing page of stories. It's all in red but the readability is maximized. Change the red to your blue theme...and you have a good simple template. With the room to add all your new additions as well.
See where in the editing page it says "Share your story" make that the story and group title.
Below where it says "contribute your story" make that the author information. Below that, have your tools and information. Then the story. Then below that is the stories information/time stamp, then the extra tools of reactions below that. By doing that you optimize your left to right reading which would draw more attention to the ads on the left...if that's a desired reaction. And readers wouldn't mind because there's not going to be three things for the eye to split with when reading a story. Actually five counting the added information inside top and bottom of the story portion. It shouldn't be inside that section but completely separate.
I just said in an elaborate multi paragraph fashion..."make it white with blue lines and only have your gray blue banners separating information. Same text font across the board, little variance to font size. Titles one size, information one size, and the story one size. Do not have an information/tools sidebar inside of the story section. Have it under the title and above the story."
Just for fun...some optical illusions
Update: I'm seeing you guys have done a lot of changes overnight! Whoa...now the editing page is in blue with a nice wide space to write and read...I LIKE that! It's very clean. It's plain but effective when doing a lot of reading. Easier on the eyes. Though I'm seeing the group stories are red which I think is temporary? It looks like you guys are doing a lot of changes right now. I wonder if you have screen shots of all your old formats for comparison?