Both transmission and rtorrent does not really scale all that well when you have a non-insignificant amount of active torrents.
rtorrent, at least 1+ years ago when I tried, seems to assume that disk reads are basically instant, and does not queue them very well either, which really helps when you have a multi-disk raid.
it went to 100% CPU when sharing to a low-thousand number of peers, almost all time spent in kernel (select, it seems that they are not using epoll). And since the disk is mmapped as memory, accesses to it is blocking. So in essence only one read is done at once.
The again, I guess they work just fine for "normal" amounts of torrents (and bandwidth) even if they are inefficient.
I never got transmission running correctly with my torrent list at all.