I've had both a Mk2 16v and a Mk3 16v and both engines are good, but to compare them properly you'd have to put them both in to identical shells with identical mods to see which was better performing, or more to the point, better for your driving style.
Mk2 1.8 16v engines are cheaper and cos they were mechanical injection, they have less to go wrong, the Mk3 2.0 16v has electronic systems that can go wrong and mine had plenty of issues which is why I got rid of it.
If you're putting it into a Mk1 shell, I'd probably go for a 1.8 16v as it seems like an easier swap and definately cost less than the 1.8T 20v.