Yesterday, Comcast tried to start charging me 2.5x for my Internet service... I called to cancel the service and all of a sudden, they were able to give me the old price...
I have custom DNS setup, that didn't seem to improve it much.
BTW traffic being faster in a VPN is pretty common for ISP throttling, for whatever reason.
But like you said, it's not useful to us as a customer of an ISP because we can't alter the routing table used by the ISP even if we identified a problematic routes/peers. You can try to complain to their customer support, and might get lucky if the customer support has technical authority to debug peering issues.