I've been having a lot of graphical problems with this game. The flickering and aliasing are common, but they are not anomalies, but merely problems caused by the ancient hardware. The shadowing is another issue. The shadows are jagged and flickery, and take time to load.
I've never seen and read about anyone encountering such a problem on this game or any other. This problem has occurred on this game, and all the PS3 Assassin's Creed titles (especially Brotherhood and Revelations). Revelations in particular has a lot of video noise as well - that I attributed to my HDMI port, and a service center (not a Sony-authorized one; I live in India so such places are uncommon and expensive) concurred with my judgement and removed the port, told me it was broken, and said that they would look for a replacement, advising me to use component cables in the meantime.
I did buy a set of component cables and although the graphics do look better (my Assassin's Creeds are with my friends, so I haven't got the chance to retry them) and the noise has entirely disappeared, the jaggy, flickery shadows do remain. I tried reducing the sharpness on my TV, and the aliasing has reduced everywhere but the shadows. The shadows are somewhat like this:
Does anyone else have a similar problem? Is my PS3 broken? It's not in warranty anymore. How do I get rid of them?
'You never give me your money, you only give me your funny paper. And in the middle of negotiations, you break down...'
Yeah I got those shadows too, it's just the nature of the beast. That's how they were in RDR too. What annoys me more is not that they are jagged, but if I am, say, running parallel to a wall the shadow will draw itself just a few feet in front of my character and disappear a few feet behind him, like it's keeping pace with me. Very annoying, but as you said, that's how it's got to work with this hardware.