is there a way to keep the object complex but simplify the number of paths that I can set keyframes for or am I asking too much?
show us a visual example of a shape you want turning to another shape so we will have a more specific recipe for your case. i.e show your two shapes side by side either in Ai or Ae
What Roei said. Without seeing your shapes and more info on what the animation is supposed to look like, nobody can help you optimize this.
Go back and edit your AI files so that the white cutouts are all connected by a small (outlined) stroke. Then merge the shape so that you only have one path for your white. The black can then be made into a single object as well, which encompasses the entire space of the artwork (basically a filled in outline of the entire graphic). Then you will only have 2 paths to deal with for each graphic. It might help to separate the white pieces into a few more manageable blocks that roughly correspond to a common size, shape and area between graphics, since with only 1 path, you'll definitely get an unpredictable interpolation between the two.
It sometimes helps to copy your shape paths to a solid layer so you can utilize the "mask interpolation tool" or whatever it's called (it's a UI panel in your windows menu). The mask path interpolation tool can perform more location based morphing versus shape layers which can only morph based on numerical point position and direction. You can play around with the settings in the mask tool, like adding intermediate points so that there's more points to flow. When you've gotten it looking how you want it, just copy and paste the keyframes it creates back into your shape paths (you'll probably need to select them all and reposition them).
The reason I say to connect the white pieces and make the black a general shape is that this way, your black outline will be much easier to give you a seamless morph transition, while the white details will mostly be a pretty wild transition. If you were to simply make the whole thing a single black path, you'd have no broad shape to carry your transition and it would be much harder to get a good result.
You can also play around with adding a few effects on top of the details morph to smooth everything out. If you add some matte correction effects, you can get them to sort of blob together into a liquid-like state during the transition so that you don't see a lot of jagged edges crossing paths.
Ultimately, it would serve you well to try and simplify the details on those graphics, as they really aren't very conducive to shape path morphing.
Morphing all of those paths is going to be a problem. The only reasonable way I can see to do this is: RE:Flex - RE:Vision Effects
If you want to morph paths you'll have to completely redo the artwork and simplify it. Then you could use Illustrator and blend to generate a morph. Here's a tutorial I did about a zillion years ago that explains the technique: Morph In Illustrator and AE.
And here's an update quick look at the morph using Illustrator and AE that I did a little while ago showing the basics.
Thanks for all the tips everybody. I now have a better grasp on the capabilities and restraints of morphing.
This tutorial video is just brilliant. Thanks a lot!