I have both versions. I like the unit balance of original better. I like WE's halved production costs for buildings. Doubled geisha production time makes it easier to play Expert without having to deal with tons of enemy geishas running amuck during the late game.

Most of all, I like the additional campaigns that WE offers (1530, 1550, 1580). I've had Shogun since it first came out and play it more than any other game, even now. The standard Sengoku campaign had become a bit boring, and the additional campaign scenarios were and still are a delight. The Mongol campaign is just ok. I play it for kicks once in a great while because I enjoy using Mongol cav.

I don't trip on the "fantasy" units, I just don't use them much. The AI rarely produces them, so that's not a problem. I do use Battlefield Ninja, but only a single unit mixed with an army when I feel like trying to ambush the taisho, or, one "army" of nothing but ninjas (Tokugawa 1580 campaign begins with 9 units; I put them all in one group). These I use to raid, draw a larger enemy force where I want them, or to attack/assassinate a poorly protected daimyo or heir. I limit myself to the one group, and don't build additional units unless they suffer a lot of attrition.

The additional campaigns scenarios are what I like best about WE, what make it my choice over the original version.

For multiplayer, the Samurai Warlords mod for Medieval/VI is still my favorite.