The "throttle" action has been coded with some poor choices, which are now slowly coming up and producing errors. While all subtasks provide some information about what is wrong, the goal of this task is to coordinate such a delicate overhaul. Below is how I'd envision fixing this up, but any other thought will be highly appreciated.
=Proposed workflow=
# Merge [[https://gerrit.wikimedia.org/r/#/c/mediawiki/extensions/AbuseFilter/+/458135/|this patch]] to avoid some tricky problems in new filters
# Merge the patch for T203336 to start reducing errors
## Execute the included maintenance script (to be checked carefully, it could potentially change many rows)
# Devise a clear process to start deprecating old syntax (first phase of T203359)
# Assess the risks of having a comma inside throttle parameters (T203585). Do whatever is necessary to make it safe.
# Use a new, safer syntax for throttle parameters (T203554) to avoid problems like the one with commas, the one resolved at point 1, and T203535.
# As in point 3., apply the devised deprecation process to the code related to old parameters.
# Address the problem of having empty throttle groups (T203584). Find a way to fix it (discussion on task). Duplicates are handled in point 2.
# Wait a few MW releases, then remove all back-compat code.
Any proposed workflow (included the one above) should be carefully examined to avoid any error at any cost. The code already has enough problems without adding others. All but point 8. should really be addressed ASAP.
As for other subtasks not mentioned above:
# T196995 is a minor proposal for improvement, mostly for better clarity
# T24623 is a proposed improvement to avoid throttling too easily
# T195699 is another throttle problem of which causes haven't been determined, and which could get fixed during the process of this task