That's a good question, and there aren't any official answers on the matter. You can sort of infer the differences by sifting through the marketing materials and comparing ATB/road models from the same maker... the following trends seem fairly consistent:
When designing MTB pedals, the ultimate goals are the same as with road pedals -- easy, comfortable entry; good ergonomics (float, proper tension, etc), security, and low weight. The only real challenge present that doesn't apply much to road riding is debris, and dirt -- so I've always assumed that a good MTB pedal is designed to function like a road pedal, fighting-off the comprosmises imposed by making the thing dirt-proof.
Look at the top-notch offerings by Time, for instance. Their top-shelf MTB pedal certainly fufills the above demands, in a minimalist design that has got to include some trade-offs over, say, the Mag Impact, which sports a more complex binding mechanism... where increased durability and dirt-resistance aren't an issue, there's got to be greater ability for designers to generate more float, more adjustability, and so on.
Eggbeaters are a good example, from what I can tell. They're designed to be absolutely debris-resistant; the mechanism is so simple, you've got to appreciate the error-proof elegance. But a pair of Eggbeaters will never function as smoothly as a well-tuned pair of Impact Mags, or offer as much float as a pair of Speedplay X2s.
Of course, for most people, good MTB pedals are, frankly, good enough. Even so, unless dirt-riding (or the desire for walkable shoes) compells you towards their tradeoffs, I'd just as soon ride road pedals.
