[I have a proposed amendment to your idea at the bottom. Sorry for the delay.]
I think there’s a very large concept that at the center of this problem. Why do people comment at all? Some people comment for the sake of being featured (which is still a very good thing). Others comment to give advice or point out flaws in the story, yet other have a mixture of both. Nonetheless, there are many comments that have been submitted that have no chance of being featured and not particularly helpful that are submitted anyway.
This brings us to the question of why people comment without the goal of exp. Without the exp goal, there only reason that can encompass the other two categories is that the story motivated the reader to comment. For example, first time (and competent) publishers have a great deal of comments for their story. Why? Our community wants to encourage the author and help him/her improve. For example, my first story had four comments in which were extremely helpful for my future projects. In fact, I was quite happy with just about every comment. If my comments would have been full of short, approximately four-word comments, I would have been discouraged. I would have seen that my readers did not feel motivated enough from reading my story to do anything meaningful. Instead, they rated and commented on it out of more selfish ambition: gaining arbitrary points.
Now, the intended goal here is to increase the quality of the site which is obviously something we all want. Let’s say your idea works: each cyoa receives longer and more comments without undue work for the mods. This may still not improve the site, or at the very least it wouldn’t help me (which I’ll get to later).
First, there are the rather worthless comments that people would give. Heck, I could make over 1,000 points by just saying “This game is good” or “This game is bad”. This is minimal effort for a large reward. In comparison, EM’s Rouges is taking a massive amount of time with the reward of 123 points (100 for the featured story, 10 for being published, 3 for the daily commendation, and 10 for being most commended). Why would authors wish to write when commenting is such an effective way for gaining points? Thara gained controversy simply for racking up an insane amount of points without publishing a single story. (Note: this is not a criticism of her. I am simply using her as an example.) I hate to see somebody not contribute anything beyond simplistic comments and rating a storygame (which can be done without reading anything by randomly clicking links until one finds the ending).
Second, are comments truly this worthwhile? CYS is a writing site, thus we want to write and improve out writing. Comments are integral parts of this site, but reviews are better. To clarify, we all want somebody to post a meaningful and notably long comment for the work that we’ve put so much time and energy into. Giving a point for any format of comment wouldn’t be that much of an increase to the worth of proficient commenting. Instead of having a featured comment giving one point, it now gives two (or three after rating the story); meanwhile, instead of giving nothing to the author (or one point after rating the story), a tiny comment would give two points (after rating the story). This means a featured comment decreased from giving 100% more points than a non-featured comment to just 50% more. That is not fair to the featured commenters when considering their effort.
Thus, I wish to propose an amendment to your plan which would eliminate the blemishes that I believe currently exist. Perhaps, the length of the comment has to be high, about 80 words or 400 characters using a validation method, in order to receive that point. For example, the first paragraph is 79 words, 364 characters, 442 and characters with spaces long. A comment of that length would be long enough to be either: A. meaningful or B. random ranting and thus quickly deleted. This way, the short comments will not receive points, the comments that are featured anyway receive a point, and those comments which are still long yet aren’t quite good enough to be featured will receive a point as well. In essence, good comments with sufficient effort will be rewarded while those short ones won’t be.