I am not questioning your experience but for the packages that I used (I just counted 63 on my desktop), I haven't noticed any of these problems.
The only grief I have is that I have a bunch of VMs (<10), and if I set them to all update all their packages simultaneously, I get rate limited by chocolatey and need to wait a while for my IP to be unbanned. But for a free service, I can't really complain.