I prefer Shogun II over Empire, but still, Shogun II isn't better than Rome or Medieval II, in my opinion, and Medieval II is superb with some nice mods, like Stainless Steel, Rome on the other hand is already awesome without mods and just the official patches. To be honest I only played Shogun II for approximately three hours so far, I got it because it came with my 2600K from NCIX.com during a special sale, so I registered it on Steam and gave it a try. It's more polished than Empire was on release, as of now Empire (not Napoleon) isn't exactly bad, but I just never liked the era, gunpowder and canons just don't cut it for me, I need raw army clashes with swords and shields and arrows, give me that any time over Empire.
Additionally, I prefer the micro-management of your empire in both Rome and Medieval II, Empire's management of your forces and resources was streamlined/simplified, I never understood why since it was working fine the way it is in Rome and Medieval II, I guess they wanted to change it for the sake of trying something new, who knows. From what I've played of Shogun II it does feel better overall than Empire (the management), but I haven't seen enough of it to say that it's more or less streamlined than Rome or Medieval II, what I can say however is that despite the beautiful graphics what I didn't particularly liked about Shogun II is the scale and size of the world map and the soldiers on it, everything is really big... maybe it's my resolution, heh, but anyway Shogun II isn't bad at all, a solid game, but after trying it about two times I never bothered resuming, I lost interest right away and I haven't played it since, and it's still installed right now.
I'd say if you want to give it a try then perhaps wait for this year's holiday sale on Steam, or get it from D2D if it's on sale or something. If you don't mind paying the full price (I'm not sure of its current price) then go for it, it's certainly better than Empire, in my opinion, but Rome and Medieval II are much better. I loved Rome and Medieval II is awesome as well but it's much better with modifications (Empire has mods too, but whatever mods are made for it it won't change its era and the game-play mechanics that goes with that).