Okay... I'll try to stay away from comments about the lighting and the posing, as those were both out of your control, particularly with limited time with each animal. I agree with you that 3 and 4 are my favorites of the set.
1) I agree that a tighter crop would have helped. I certainly would crop in from the right to remove what looks like a wooden pole - I probably would crop all the way to the edge of her cubby hole. I also would crop from the bottom to remove a good chunk of the grass - because it's so much more brightly lit, the eye is trying to be pulled that way. If you had composed the shot this way, or planned to crop it like this, you could have increased your exposure and the orangutan would have been better exposed (who cares if you overexpose the grass if it's not going to be in your final image?). I don't know how your post-processing skills are, but I'd try to either clone out or at least burn the dead grass clinging to her hair.
2) I would have shot this with my aperture as wide open as I could to try to maximize the blur of the background (it's possible you did this - can't really tell without knowing the relative distances of you to them and them to the fence). It does look like there is a tilt to the image. It's possibly your camera was completely level (elephants lean, and the fence may have been running slightly uphill or not perfectly perpendicular to your field of view), but there is a perceived tilt. I'd try rotating the image a bit clockwise, you should still be able to recrop it for a decent composition.
3) Probably my favorite of the set because of the use of color. I like that you didn't zoom in too much, I agree with keeping the lily pads in the shot. It's unfortunate that you have the bright spot on the lily pad directly above the frog as that draws the eye. You also would have been better to compose with the frog in the lower right corner, perhaps even beyond a rule of thirds position. He's lined up almost perfectly with the diagonal of the image, so moving him to the lower right would have created the story that he is looking - and perhaps getting ready to jump - into the center of the frame.
4) Nicely timed capture, it looks like he is looking directly at you. However, it looks like you used a far-too-shallow DoF here. His face is relatively sharp, but the rest of him, from the top of his head back, is out of focus. That being the case I'd actually suggest cropping in extremely closely. Let his face fill (or essentially fill) the frame and lose the out of focus parts of his body.
From your post I'm guessing you're getting a handle on composition. Just remember that the Rule of Thirds is a good suggestion but not a law - there are some times that a central position is best, or an extremely off-center position. Next is to learn the exposure triangle (aperture, shutter speed, ISO) and to adjust each setting to get the effect you want while properly exposing the subject.