Just my 2 pence...
I agreed with the multi-quote previously (for reasons mentioned above), but now with post ratings, I feel that keeping replies separate has value - for slightly different reasons to the OP..
I find ratings very useful. I'm one who misses them on Front Page articles. I found them handy to gauge not only general community consensus either positive or negative on a topic (sometimes it wasn't obvious whether the information in an article was good or bad), but it also let me see (crudely) the level of interest of an article by simply seeing the number of votes.
When I'm short on time at work, I'll scan the article comments and read the ones which are voted highly negative or positive - thus keeping my focus on comments which are likely to be thought provoking, insightful, funny etc and steering away from the more mundane ones.
When I have more time and I'm reading MacRumours at my leisure, I'll join in and rate individual posts up or down. However on a number of occasions, due to multi-quoting it's split my opinion on whether the comment is good or bad.
For example, take a comment with a 3 part multi-quote reply. The first bit of the reply may be very useful info which I would like to flag as positive to highlight its worth to the community. However the remaining 2 parts of the multi-quote reply contains incorrect info - I'd want to down-vote this info. With multi-quoting I can't separate the good and bad in the post. I either up, down or don't rank the comment. If I up-vote the comment bad info may be seen as positive to the community. If I down-vote then good info may be lost. If I do nothing, the bad info may be seen as innocuous.
In the grand scheme of things it seems minor - but let's say the above fictional 3 part response detailed information on re-building an iPhoto library. The first bit of info may help users of the forum salvage photos which may other wise be lost. Following the 2 bits of bad info in the multi-quote reply may result in permanent photo loss. To inexperienced computer users looking for info on the forums these votes may be of importance.