Mm.
Something about ads.
That and there were some software bloat for unnecessary functions and the like. uTorrent became super popular because it was a lightweight, Just Works client unlike how Azureus was, so as it "grew" people started asking questions. Many have experiences that uTorrent 2.x is faster than 3.x (I didn't really notice myself*). There is also the "sellout" aspect as the original Bittorent, Inc. bought uTorrent.
*DO NOT, however, use anything older than 2.2.1. There are well known security exploits.