I don't understand. The sidebar alerts works exactly the way you have described.
1. When a thread has a new reply, the alert will appear in your sidebar. (support for watch threads is being added next week)
2. This is currently how the sidebar works. When a new thread is opened, the forum shows "NEW". The forum list show the last 25 forums you have visited. Maybe your visiting more than 25?
3. This is currently how the sidebar works. You can click threads or forums with alerts or mark them as read.
No it doesn't, I already pointed out the difference.
1. When a thread has a new reply, the alert will appear in your sidebar. (support for watch threads is being added next week)
BEFORE: Threads that I added to watch list would trigger alerts on new post.
NOW: Threads to which I replied at any point in the past trigger alerts in the sidebar.
DIFFERENCE:
1. I had complete control over what threads were in this list, but now I have none. I could manually watch threads in which I didn't reply and I could not watch a thread in which I replied.
2. The alert would trigger once and would not trigger again until you open the thread. In the new system every reply bumps the thread to the top of your list, regardless if you viewed it or not.
WHAT TO CHANGE: The sidebar should just use the watch list instead of having another separate list of threads.
2. When a new thread is opened, the forum shows "NEW". The forum list show the last 25 forums you have visited. Maybe your visiting more than 25?
BEFORE: You could watch a forum, for either new posts or new threads only. If you select threads only, you get alerts whenever a new thread is opened. If you set posts, it's the same as if you're watching every thread in that forum.
NOW: There's a recently visited list that shows some forums and shows a "new" tag if it has new posts but that's not the same.
DIFFERENCE: Each new thread triggered an alert which had the title and link to the thread, as well as the user who made the post. Here I just have a "NEW" badge and have to open the forum and check what's new myself.
WHAT TO CHANGE: Same as 1, that change should automatically fix this issue as well. Recently visited section is pointless in it's current form and can just be removed.
3. This is currently how the sidebar works. You can click threads or forums with alerts or mark them as read.
I can't mark all as read and I have to click the white circle on every single thread. Mark all is needed. Previously I would watch a certain game forum because I'm interested in buying a certain type of account. Most alerts that I would get could be ignored, since it's either not the type of account I'm looking to buy or it's a buy thread. I'd sometimes have 5-6 alerts, neither of which interest me, but yet I still want to get alerts for that forum since occasionally the exact thing that I'm looking for shows up and I don't want to miss it.
So the main change to make would be for the sidebar to use your watch list and not simply all threads that you ever replied to. Watch list ONLY, not watch list on top of whatever it's doing now. Then the user would have complete control of which threads show there and can set it to show only relevant content.
And for the "My active threads" part I don't see why they wouldn't be sorted by bump time if that's how they worked before, whether intentional or not. Just because you don't want it or use it doesn't mean that others didn't. It's still a feature that got removed and the experience is now worse.