There were a couple of ideas posted a while back that had home made practice pad ideas even for the kick pedals.. all you actually needed was a pedal and you could modify it into a practice pedal.
Not sure where that thread is now anymore...
If you can afford an E-kit, go for it. It's the closest you can get to quiet drumming.
If you can't, practice pads are the way to go. And foot exercises can range from muscle exercise to coordination exercises. Nothing can truly replace the feel of a pedal but it doesn't mean you can't practice without one. (For more specific ideas you can drop me a PM)
Remember, practice on the drumset is obviously the best option, but it doesn't mean you can't practice without it. Practicing drums ain't just about playing the drums. Just like how training for the 100m dash doesn't involve just running 100m over and over again. There are all sorts of cross training exercises you can do.