Congratulations on making it this far!
However, I'm gonna have to say I'm not a fan of the layout. On the main page front: Color-wise, it's much too busy; I can't follow it very well. So much is vying for my attention that I can't focus on any of it. Looks like it's the sort of design where it's easy to get to the newest stuff but very difficult to see specific articles, which is bad for people like me who like to read everything that goes up. I have a long-standing and highly personal grudge against the sort of time-based navigation thing that is used to link to individual articles.
As for the individual articles, call me old-fashioned, but I liked having all the articles in order and linked to each other and being limited to a single print-like page at a time without scrolling. It was part of the charm, the sort of thing that lets you know "This is different than the other game sites." I liked that they were sorted by issue. The magazine metaphor was very distinct and very strong previously, whereas now it's sort of coming off as an imitator of 1up.com [http://1up.com]. And, really, if you're going to imitate a website design, there are far better ones to choose from. I understand the reasons why several pages of hand-drawn art accompanying each article would be too expensive, but there's no reason to throw out the very logical, elegant interface that surrounded it.
Anyway, now I'm worried that I will miss articles from time to time. I'm sure you don't want that. My suggestion would be to keep having an index page for each issue, sort of like the cover pages that previous issues had, and give us a big old prominent link to the most recent issue rather than to the individual articles. In my mind, the reason that I keep coming back to The Escapist was because of its very distinctive "magazine" metaphor, with the main articles each week adhering to a central theme. The current layout is like cutting the articles out of the magazine and scattering them around. It may be easier to get at each one, but it's jarring and it doesn't match the style of content you're delivering.
And while I'm on the subject of criticizing the layout, there's not much I'd change on the forums themselves, aside from the colors. Certainly make thread titles bold, or do something to make the "new" indicator distinct from the thread titles. Maybe make threads with new posts have bold titles?
Just my two cents.