It's a tough question for me.
I think Shogun 2 has the best system, mechanics and AI and I think the difficulty curve (for once) is handled really well, thanks to realm divide and the taxation system, it doesn't feel so much like the difficulty drops away as your faction grows, which has always been a problem with total war games.
But nonetheless, I have a dark, guilty love for Empire. It had a really bad release, but it really stepped into its boots with subsequent patches. I love the scale, I love the potential for counter-history (yay British republic!) and it's the only time period where having armies conquer large swathes of the world actually makes historical sense. Sure, there's still a lot of flaws, but I'd love to see it get a sequel eventually.
They really could have done with ripping off Imperial Glory's annexation system though. I don't think anyone would have minded since Imperial Glory was itself a massive rip off of the total war franchise. Basically, it always bugged me that as soon as you conquer a country it seems to suddenly become culturally and militarily identical to your home nation. European countries have never really conquered each other in that way, it's always been about puppet states and coalitions and vassalage, which I think IG got across (just by letting conquered countries keep their uniforms - albeit historically inaccurate uniforms - on troops recruited there) in a way no total war game ever has.
I don't think such a system would be too hard to mod actually. It would just require a metric fuckton of new unit entries.