A few things:
For the "Recent Threads" on the sidebar, I kind of like the icons indicating what type of board it was in, whether it was in General Discussion, NDS, Wii,Ofon the main pagef Topic,...
I found that nice, so I could see what type of thread it was at a glance.
Second, I do kind of miss the medals. Not a big deal, but I do kind of miss them.
Third, the color changes. It does not bother me that much, but I was used to and liked the old color scheme.
Suggestion for the color scheme, as I know that the site just cam back up and you are working out the bugs. Maybe add an option to the "customize page" option where we can use custom CSS to customize the front page how we like it, so that it is easy to use for each person. If you did enable custom CSS, perhaps have a few different "Styles" for people to choose from, or use/make their own.
In terms of the customize page, it would be nice if there could be a "Preview" button, to see what it is like before you save it.
The new style of everything is different and a lot slimmer. It seems that a little hard now, as I am discovering the features of the board again, but I will grow to like it.
I do like that the search does not give an error anymore when searching for a game with a number in it, such as Black and White 2. That had annoyed me with the old board system, where it wouldn't accept it because the "word" was less than three characters. I enjoy the new board, and I am glad that GBATemp is back.