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!
Private Mod Note
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Village Mechanics: A not-so-brief guide - Update for 1.4! Added subsection on iron farming to the iron golems section. Only ten villagers required to spawn golems (down from sixteen)! Put to rest the "facing doors cancel each other" myth!
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.