I don't like all the boxes that blow up on the screen when you roll your mouse over them. OK when on the front page, but when you're further into the site (like MMB) and they're still jumping out when you roll the mouse over them it's annoying.

MMB looks much better - visible breakdown of baggage allowance and improved seat selection as mentioned above.

I don't use SQ or UA so haven't been on their websites, but eightblack's comments surprise me as I don't think EK have had a well thought out or implemented site for a long time, so I'm surprised there could be worse. Let's hope this version performs well.