I went through similar problems with Ubi's own download manager on the free Far Cry 3 I got in the AMD 4-in-1 game bundle with my 7970. I've been diligently putting every non game program I can on the E partition of my new 128GB SSD. Since I left only 30GB for the OS on the C partition, you can imagine what I thought when the download process for a fairly large game file doesn't even ask me where I want to put the install files.
So I end up stopping the download, then starting over. This time it allows me to choose a location, but by then I was pretty pissed, so I forgot to make a folder for it. Then again, I was kinda expecting it to have a shell folder, vs sprinkling all the install files all over the place. So I stopped it yet again.
Then it doesn't want to give me a location, then back to giving one, but I actually had to stop it one or two more times due to it having a problem locating and/or downloading certain files. Finally I got a full download in and successfully installed the game where I wanted it. I have to wonder though, given all the problems I'm having, if it's only poor optimization or corrupt game files from that crazy download process, or maybe both.
Oddly enough, AC3 is about the only game I've played lately that hasn't given me crashes. I've had crashes in FC3, Sleeping Dogs and Hitman Absolution, but mainly just FC3 and SD. Hitman seems to have no problems now that my C++ updates are installed, but SD and esp FC3 have made me disable my OCs, which doesn't set too well with me given the time I put into the BIOS settings and the performance loss I'm now getting.
I can see why a lot of people prefer Steam for games they download. It has a lot going for it and works far better than Uplay or Origin.