Disadvantages of rTorrent:
* CLI only and no easy to use graphical interface (unless you use ruTorrent)
* Might need to install VNC anyway if needing a graphical browser to add torrents.
Disadvantages of uTorrent on Wine:
* Must install x window, VNC, Wine.
* Uses quite a lot of memory running all those behind.
* VNC not as secure as putty (SSH)
* .torrent file associations never stick.
* A year ago had problems downloading torrents with files in different languages (not sure if still a problem).
So my vote is rTorrent with ruTorrent web interface. Can run on very low specs!
If you are going to run uTorrent though make sure you use fluxbox and not something bulky like gnome for your gui.