I really wish they could come up with a way to rate threads based on the people that are participating in them. I don't think they currently use the "rep" system at all, but wouldn't it be cool if you could sort the current threads by some score that was based off of the rep system? So when people that have high rep post to a thread, it scores it. Then you could have half of the threads on the first page based on their scores and the other half would just be new threads.
I think a lot of interesting topics are being lost in the shuffle lately, but maybe it's just me.
Unfortunately as you seem to know already, rep's kind of broken. It's easy to max out, and if you just post a ton you'll eventually get the same great rep as someone who's only posted 10 times but every post was solid gold. It's also kind of a popularity contest, you can get it just for stating obvious stuff that a lot of people agree with. Or for posting a funny pic in the gif thread.
Really there's no way to predict when a thread will be gold, or will start out bad and then turn into gold.
There are a couple of ways you can follow good threads before they get buried though.
One way is to use ignore on guys you feel start junk threads that you never need to see. Another is to use the subscribe feature. I think subscribe is a little clunky though. I think you should be able to simply click a single button at the top of bottom of the page to subscribe to it, and then the next time you're in the main forum... all subscribed threads will appear at the top of the list right after the sticky threads.