Merge the "Queue Manager" into the main window.
Just add the "Order" field and then you can sort by it.
Make sure the order can still be changed.

This should get rid of a lot of duplicate code and make it more intuitive/easier to use.

KTorrent is my favorite client and this is currently my only big complaint with it. Having two complete lists of torrents with just slightly different levels of information and uses is really annoying and counterproductive. Being able to order the queue in the main window would be so much simpler. For example, when having many torrents lined up with various levels of completion it's unnecessarily bothersome to order them after completeness. If it was all done in the same place it would be possible to just simply drag them to the right position after a quick glance at the progress bar. I think that many people would appreciate this change.

Another queue related change I would like to see (but not nearly as much as the previously mentioned feature) would be the option to make exceptions for single torrents from the "Decrease the priority of torrents which are stalled for too long" rule. Sometimes you have that single, extremely slow, yet important torrent that you want to finish as quickly as possible even if it is stalled for prolonged periods. But at the same time you don't want to waste time with all those other downloads that share the same behavior.

Other than these two things...
Thanks for a great piece of software!