MIMF

I have a Wasburn acoustic that has a transducer under the saddle. The saddle is sticking up too high and causing the action to be too high by a mile. The saddle is also loose in the slot and leaning forward causing the intonation to be off. I took a look under the saddle and the transducer takes up so much space that there is less than 1/8" depth for the saddle. I believe the guitar was manufactured this way. The bridge is also only 1/4" thick. I need to lower the action and I think all I can do is take it off the bottom of the saddle. There is room at the nut to lower it a little but that won't do it all. It just seems wrong somehow. Should the bridge typically be heavier on a guitar like this? Not sure the transducer can be lowered. Any suggestions would be great.

Take out the pickup. If you have to, put in a better Fishman type that is thinner, or even a K&K pickup that doesn't go under the saddle. And make a new saddle.

Can you deepen the slot? I would also make a new saddle that fits properly.

It is possible to do all those things, but first lower the strings at the nut before making any other adjustments, THEN adjust the relief in the neck. Only then will you be able to see how much you need to remove from the saddle height. All those adjustments are inter-related and each is dependent on the previous one, and they can all add up to a significant improvement.

I agree with Mark regarding using a pick up type like the K&K, as it doesn't got in the saddle slot, so that will gain saddle height reduction of however thick the under saddle element is.

Remember that the saddle should be free to move up and down easily if you are using an under saddle element, but if you choose to use the K&K or similar the saddle should be snug in the slot.

You should do the things Michael mentions first, then lower the saddle. It only needs to stick up enough to clear the front of the bridge (assuming it still has some down bearing). If the action is still too high then the guitar probably needs a neck reset (the bridge is already a bit low).
If the saddle sticks up only 1/8" above the bridge then 1/8" in the bridge should be O.K..