Removing the colors makes the content pop, but it also makes the site look really boring and the extra padding/margins around elements seem pointless.
I don't think Newgrounds needs to have the typical slick/modern, tile-based layout as every other site but I really hope someone at NG has time to just play around and prototype this stuff.
UX/UI is the #1 priority of a site which already has content-related stuff going for it. Not saying it should receive the most time invested into it, but there should be a day a week, or a few hours every now and then where someone sits down and talks about/prototypes new layouts or sections + the themes.
With modern web tools, that stuff isn't really hard.
I'm not sure how difficult the site would be to modify to adapt it to layout changes. I recommend just making something work and then learning, over time, the best way to refactor difficult code. Sometimes, rewriting very small portions at a time and using new code, slowly fading out old code (ex: replacing only one instance of old code, rather than all similar instances and seeing how that works) is all you can do.