Well Nancy it sounds like you changed to get to the wood, but the wood blows.
I see a few choices for you:
1. Paint the wood floor. Sounds like a sin, but it might look great depending upon a ton of factors. You might even be able to get a dark stain to cover the pet stains, check with a local paint/stain supplier. or ask Mr. Paint.
2. Apply a prefinished wood flooring over the old floor, or pull up the old floor and put down new wood. Depending upon the dimensions of doors and other factors, this may or may not be possible..