CMS WordPress is quite an adult - it has grown to version 2.5.1 and almost completely lost its old bugs. But novices (and not only) every time they install this engine, they step on the same rake.
The fact is that most bloggers come from LiveJournal, in which a tree of comments is a familiar and convenient thing. But in WP with this historical problem. The last couple of years in young blogs with the same frequency and consistency there are notes about problems with long-suffering comments.php, which can not be divided by different plug-ins, each of which, in principle, is necessary. The branch WP function has not entered the branch function in the comments.
Plug-ins that grievely implement branching:
Brian's Threaded Comments - implemented in JS, with distorting the code and turning the installation of other plugins into shamanism.
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That seems to be all. Advise, great ones, what to use - what would the comments work normally, and it was possible to answer, and plug-ins for working with mail, OpenID and others while still alive? Or maybe it's time to write the desired piece and add the authors to be included in the core? I bet, thousands of thanks will be said, and I will be among them.