My suggestion is get rid of the horizontal pinstripes in the header/title bar graphic, keep the J2O logo and background of a JJ2 level, remove the Daily Carrot logo and use a backdrop of polka dots in any color, but not yellow because yellow is overused in J2O.

That way it's more of a graphic patch than a layout overhaul. But one aspect of the layout that seems inconvenient is that there are essentially 3 panels on the front page, news in the middle, sidepanels on the right and site sections on the left.

The news in the middle is by far the longest part. The sidepanels on the right are about half as long, and the site section links on the left is very short. That's a very imbalanced approach to looking at a website, reading the news makes you scroll way further than anything else, and the left side of the page is underutilized.