NOTE: Sometimes it's hard to figure out what you're describing. Please take screenshots and cut them down to the effected area and post them. Thank you for helping us help you help us all.
Now, let's see if I can cover some of your points without a lot of specific quoting.
The box in the upper right corner is user navigation. It's a new and very integrated feature in IPB 3 that we'll all have to get used to. To be honest, I don't like it either. It's probably the single biggest thing I don't like about the upgrade, but it really isn't that bad.
The vertical line between userinfo and post and the horizontal line between post and sig do need to be darker. This skin has been fixed, I'll look at the others later.
The emoticons are formatted as the IPB 3 template came. I'd like to see them closer together, perhaps 4 to a row, and yes, they will be separated again or sorted in a better way.
The spacing (padding) for the forum list is being checked on now. It is a lot to scroll through, but it may not be possible to reduce without making other areas too compact. We'll see what we can do.
The old division between pinned and unpinned topics was removed by IPB in the upgrade. It can be restored with a great deal of effort, but the idea is that people never respond to pinned topics and often don't even read them. We've noticed that to some extent here, so they may have a point. Give it a few weeks and see if you adjust, and we'll take the same time to see how it's working out as well.
The Technic post font is now considerably darker. It didn't seem that light to me, but this will certainly please everyone.
"Previous Topic | LEGO History Theme | Next Topic" is a tricky problem. The new system defines certain links individually, then lumps others together in one setting. That set also controls the appearance of your username in posts, all active post links, all sig links, the topic title, the topic page # and a number of other small things. Some of those appear on light backgrounds and some on dark (in certain forums like History or Star Wars). As a result, a decision had to be made that created the best overall function. In this case, those buttons lost. The ultimate plan is to modify the templates to divide those into a new setting, but that is a very low priority compared to other issues since it's time consuming for little reward. Still, it'll be addressed eventually.
Bold in places. The secondary navigation ("Eurobricks Forums > Website, Frontpage and LEGO General > Website & Forums" line) used to be bold. No clue why they decided to remove that, but it will be added back. Other instances will be found and considered on a case by case basis.
Titling a post. Was that even possible before? Why?
Missing tags? Post which ones, specifically, please.