Another Brony checking in here. Pretty much what I would have said is already up on here, so I'll just reiterate a few things in case my opinion adds weight to any decision.
It doesn't matter to me if things are re-orginized, but I think they work well as they are. My chain of forum checking events goes:
Check email notifications of watched topics and take care of any new posts/business in them
Check active topics link at the top for anything new and interesting
Scan to the bottom of the main page to double check the MLP
AND tech talk boards to see if they're still bolded (I'm interested in both and occassionally will miss something in the active topics section)
The arguement of other child board threads being covered by MLP posts is pretty weak, at best. Not only is it easy to look for bolded child forum names on the main page, the MLP forum doesn't really have a ton of active topics. Sure, there are a ton of posts going on daily, but they are all mostly centered in two or three threads. So even if you rely only on the active topics link for monitoring new posts, there's no way any thread being buried could be blamed on just MLP posts since it only lists the threads and not individual posts. Even if a thread has 100 new replies since your last visit, the topic is still only listed once in the active topics.
You say the MLP sub-forum is getting a lot of activity, right? And the other sub-forums are kinda so-so. 
If the MLP community is getting a large amount of traffic, then wouldn't it make sense to leave it where it is as it tends to act as the "anchor" so to speak for the whole Communities forum area? If we leave the MLP sub-forum where it is, then maybe people will take the time to browse/migrate from there to the other community sub-forums.
In other words, MLP tends to act as a sort of "lighthouse" or beacon for members to browse that community. And if members see the MLP community, they might take notice more of the other sub-forum communities like Furry Tech Talk, etc. and start posting there too.
Am I making any sense or did I lose you? Look at it this way. A lot of large shopping malls have what are called "anchor stores". These are large stores like Kohl's, JC Penny, Target, Sears, etc. at strategic places at the mall. And if shoppers browse those stores, then they might decide to stay long enough and continue browsing some of the smaller stores adjacent to the main anchor stores that are in the mall.
Have you actually looked at stats to see if this theory even holds true? I haven't, but here's my thoughts on the idea. I think the 4 community groups are so different that it's unlikely you'll get much, if any, cross pollenation between them as you suggest. So I don't think the MLP forum being down there is really much of an "anchor" as you put it.
I'm not opposed to a re-orginization, so long as it flows well. I think the way things are, are OK, but I can agree that there's always a better way.
