Transmission, QBittorent and Deluge are the only working torrent clients for Linux with a proper GUI. They have been developed extremely slowly and have failed to become a hot choice for users. Most people end up using Transmission because there is not much of a choice.
However, this is about to change soon. uTorrent developers have announced on their Windows forum that they will release a version for Linux soon that will provide many extra features over Transmission.
However, many users still prefer Transmission and are skeptic about uTorrent as clearly seen in the comments received on this post at OMG!UBUNTU. However, some uTorrent enthusiasts are already using it on Wine.
Now, uTorrent is the cleanest client on Windows. It has no adware or crapware with it and comes in a small size amounting in a few hundred KBs. Transmission on Linux is the highly acclaimed and lightweight client. They both are close competitors and the developers at uTorrent are well aware of this. Thus, it is expected of them to create an impressive client. No release date has been mentioned yet in any of the discussions.