What bothers me about J2O:

• Designed for low resolutions: I use a laptop and my resolution is 1366x768. Nearly half of that width is filled with a purple background instead of content. News posts only take up about 1/3 of my screen's total width and because of the 16:9 ratio typical for laptop screens, some of the long ones don't even fit on the screen.
• No themes: I'm just not a fan of long exposure to the bright yellow backgrounds of the site. Also, I wish I could keep it at least relatively consistent with my JCF theme.
• No global list of recent activities: I believe there's one available to admins but I don't know of any for regular users (I think there might be some external ones, like the Twitter feed? Not sure if it signalizes everything though, and I would still prefer one on the actual site). Some sections are updated so rarely that new contributions are hard to notice (Rabbit Journal, code snippets, articles) and it's necessary to remember about visiting each individual section.
• No preview option for text input, some of which can't be edited after confirmation (Rabbit Journal, private messages). Information about formatting used on the site is difficult to find (I think only the pictures section links to it, unless something had changed). Stijn also mentioned wanting to change it from Textile to BBCode or something else, so there's that.

To that, add some things already mentioned in Stijn's thread, such as spread out information and difficult access to some sections.