Thanks everyone so much for the feedback! I've started incorporating some of the ideas here into fixing up the pixel art.
1)
Chonky Pixel, thank you so much for all the tips! I took your advice and modified the logs accordingly. I also went through some of the tiles and removed single pixels and tried to define things better.
For the lilypads, I had originally animated them (obviously you couldn't see that in the static pic). I was potentially thinking of having glowing objects on them for the player to retrieve, so that may change up the lighting. I'll have to figure out what I do with them ultimately. Your comments about lighting are noted.
Also removed the outlines from the turtles and tried animating them with some water effects.
2)
xi, I like the shadow idea although I may use such shadows if I opt for a dusk level. I've been toying with the idea of having levels set at different times of day, so that may work.
3) On the subject of the log perspective, that was intentional to mimic the original arcade graphics. Granted the original game didn't seem to use a set perspective for objects. For this game, I'm attempting to keep things from a top down view for the most part, but I'm willing to break perspective where I feel it's thematically appropriate.
For anyone interested in what things look like now, I have a short video of the current state of the game:
https://www.youtube.com/watch?v=w1JoLAt-sEgAnd here are a couple of the current sprite maps with the various frames of animation (turtle and frog). Never done animation before, so this is all new to me: