I have the same issues; I switched from utorrent to transmission because I was attracted to the onpeak/offpeak scheduling available; as in australia download caps are split for daytime-nighttime, and offpeak- 1am->8am (prime dl time)
Sadly I noticed that my download speeds are crawling. I tried limiting connections, limiting peers, limiting downloads, uploads.
My ports are forwarded and open.
I am running encrypted peers only.
Just for kicks, I put the same torrents into utorrent, with essentially the same settings - and my download speeds jumped from <10kbs and often below 5 - to never really falling below 20, averaging around 60, and peaking at about 200.
I'm surprised that whatever the difference between transmission and utorrent is, that there is such a massive discrepancy in dl rate; especially as my upload was always maxed at its set limit (whether I set it to 20, 30, 50 or 60 - above 60 my dl starts to suffer, but even with upload limits disabled, my dl was terrible with transmission)
I'm not sure I really understand why this would happen.
I do like transmission, but honestly at the speeds I am getting, the computer resources I save dont compare to the human resources I spend on it