There's currently an effort underway to create a repository of useful pro-forma comments.
In the right hands, pro forma comments are a good thing, they fill in the gaps and educate the users about how Stack Overflow works.
Unfortunately, in the hands of thousands (if not more) of users, they create real problems, some of which I've listed below:
It doesn't feel like it is, but think of what spammers hope to accomplish. They lower the cost of sending out messages in bulk, knowing that the rate of return on their spam is less than 1%.
Everything that a proficient spammer does to increase revenue is about lowering the cost of getting messages out. The more messages that go out, the greater the return.
Apply that to Stack Overflow. You have thousands of users that might use this script. Collectively, you are all one giant spam bot. I know you have good intentions, you want to educate people (it's why we're all here) and you care about the quality of the content on the site.
But collectively, you're only reaching that less than 1% while introducing tons of noise on the network. You're actually doing more harm than you think you are.
They don't actually solve the problem.
Most of the comments here are actually pretty good. They talk about what not to do on the site, not what not to do in your code.
The ones that do talk about what to do (or not to do) in your code don't actually answer the question.
And if they did, it's a huge indicator that you have greater concerns with that question. It's either too localized (which you can vote to close on, or flag for moderator attention), or you should get your hands dirty and edit.
An extension of the above, the Stack Exchange network is about answering questions, not evangelizing, and yet, that is what most of these comments do.
I love the teaching moment, but the thing is, teaching only comes at a time when the user is open to being taught.
Many of the comments that are about code are just one-way preaching saying "don't do that." Sure, there's a useful link why, but it's not tailored to the problem at hand.
A better solution would be to answer the question as asked, but then go on to indicate why they shouldn't do that, and why the other approach is better. I've found this to be the most effective way to get people to be susceptible to learning new things.
Remember, we're here to answer, not to preach.
You reduce the efficacy of the message
Pro-forma comments make it easier to post the same thing, over and over. You know that dialog box that repeatedly pops up, in that application you use every day? You know how you dismiss it without reading the message because it's just a nag that you know you can ignore?
Then remember that day where you lost that important file because you dismissed the wrong dialog box?
When used excessively (which is what the script enables), you desensitize the user to the message. They see it everywhere and they simply ignore it because it's become background noise.
There's a reason they haven't been baked into the system yet
There have been more than a few calls to bake the pro-forma comments into the system, but they've gone unacknowledged. Perhaps they know that the feature, when released to the majority of users of Stack Overflow, could cause real damage to the site.