I'm glad people are finally discussing this instead of just spamming snide remarks in the comments themselves.
The system is still in flux and there are some bugs - it should actually be remembering your preference but that is obviously having problems. The bugs should be fixed soon, and some further refinements made.
The default (for anyone who does not set it otherwise) will be staying as score. It has some very strong advantages, such as pushing the excellent comments to the very top where people can easily find them and thus encouraging people to read the comments, dumping threads consisting of two anons insulting each others' mommas down to the very bottom, creating a more dynamic comments area where discussions not started 10 minutes after the post was made can actually garner some attention, and also totally eliminating the first post/"I'm just posting into the topmost thread to get my comment noticed" issue.
I have been considering the merits of an email monitoring/notification system for comment threads as well, so people can more easily follow the discussions.
Karma will also be incoming, for comments to start with at least.