Recently, only the occasional chicken and sheep will spawn; squids and ocelots spawn normally.
I have walked really far across a ton of biomes, and I have yet to see a cow or pig or more than one or two chickens\\sheep.
I had Mo' Creatures for a while, but i decided to uninstall it because it makes the game too unbalanced. I only removed the .zip from the mods folder, so all other associated files are still in their floating around.
I also have Twilight Forest.
The other mods i have dont effect mobs at all, so i dont think they are a factor.
Nothing is wrong. Passive mobs only spawn "rarely" anymore after initial chunk generation. There doesn't seem to be any figure more precise than "rarely," so I can't tell you exactly just how often it should happen, but it is pretty rare. Good news is that once you find two, you can breed as many as you like!
I dunno, I played a few superflat worlds last week, and sprinting across the land I saw hardly any animals. It seems like they're common at your spawn spot, but much rarer in chunks generated later. I wonder if there's a typo in the code, some parameter changed value with 1.4.