There's lots of things wrong with the skin. Before I compile a short list, let me say than I'm using the text-only skin, though from what I've seen from the r32 skin, the list applies to that skin as well (and probably others).
Overview: I approve entirely of moving the global announcement thing to a separate page and in-page pop-up, it makes things much more legible. I would however (and I've said this before) change it to something that sounds a little more professional than "important messages". Additionally, please finally introduce a quests page, it's beyond me why that info can
still only be found on the overview.
Research: way too much info on one page. It's totally incomprenensible. The usage of javascript in the previous interface was excellent, it is beyond me why it was removed. I'll get to scrolling soon.
Construction: Pretty much exactly the same thing.
Scan: Even on a 900px high page, I can't see the bottom scan and it's even worse if I've already done a scan, it's not incommon for only the 3 top scans to be visible. Why the **** do you make me scroll every time I want to do an Advanced Unit or Jumpgate Probe, which is pretty much every second time I'm on that page? The info given for each scan is useful for new players, but everyone who's played the game before knows which scan is which and for them the info is useless. Auto-hide it.
Every single ****ing page:
DEAR LORD THE HORIZONTAL SCROLL. ****ing hell, who the **** ever thought this was a good idea? You know, there's this beautiful set-up that's been used for pretty much, oh, I don't know, every single ****ing interface since punch cards: navigation on the right, header at the top. Stick. To. ****ing. Conventions.
So yeah, basically what I'm advocating is reverting every single change you made to the interface, except for the global announcement thing. Lastly,
here, use this.