So far in 2018, the AER has published 4 comments with a few more in the queue. There has been 1 published in the other top 5 journals combined (in Econometrica). Although I haven't checked, I believe this discrepancy holds for at least the recent past (5-10 years). I can think of 3 possible reasons and am wondering which it is:
1. The quality of papers is lower in AER relative to the other top journals (at least a fatter left tail of quality). So more opportunities to comment.
2. Other journals either prohibit comment papers or the bar for a comment is much higher (e.g., the comment has to completely overturn a result rather than just causing a meaningful change in the result (which is the AER threshold and is somewhat subjective)).
3. Other journals are willing to publish comments with similar standards for publication, but we're in a weird equilibrium where they haven't published them so people assume they won't. Given that comments tend to be paper and journal specific, I'm not sure I'd ever bother for a non-AER paper since I can't tell what the threshold for publication is or whether it would even be considered (as the issue is never addressed in the submission guidelines on their websites).
I suspect the answer is 2. If so, what is the preferable policy? I personally like AER's policy and openess to consider comments, which I think is much more in the interest of promoting open science. If 2 is the answer, does anyone affiliated with the other journals care to defend your policies? 1 doesn't seem plausible, although the move to monthly issues and the increase in articles may have changed things. 3 would require everyone act like me and make certain assumptions when the issue isn't specifically addressed which seems unlikely. I'm sure some people would just email someone and ask.