Oh wait, duh. Assassin's Creed 2 and Assassin's Creed: Black Flag.
Assassin's Creed 2 is more 1400s granted (But it has some of that EU4 feel since its set in the Renaissance), and I don't know when Black Flag is set but the weapons tech is about right. There are other Assassin's Creed games set closer to that time period but those two are the ones that I've played and they're considered high points for the series.
I've played the first three games and downloaded Black Flag for free--Ubisoft had a giveaway a month ago or so--but I'm currently waiting on a sale to pick up Revelations and 3 before I play 4. I'm told the story kind of falls apart after III, but I feel like I shouldn't jump games anyway.
IIRC 2 is like 1479-1499, Brotherhood is 1499-1508 or so if you count the final boss, and Revelations is apparently 1512 (with sequences in the Middle Ages.) I know 3 is set during the American Revolution, and the Steam page for 4 tells me it's 1715, so that's pretty close, I suppose.
Cossacks(1 and 3 are basically the same game on different engines) are set in the 1600s-1700s. Specifically, you can research advancing to the 18th Century(or disable that research in the game options).
Hmm, I might have to look into those. Not sure about Age of Empires -esques, but could be interesting.
It may not be exactly what you're looking for, but at the expense of scope and moddability, Napoleon: TW is definitely the most polished and fun of the musket-centric TWs. Despite what I just said, there are actually some quality mods for it which are awesome--do recommend if you're after musket warfare.
Not quite the period I was after, but I do have an interest in the Napoleonic wars, so I'll definitely look into it.
There's a Slitherine strategy game called the Thirty Years War, but I haven't gotten around to playing it yet, so I can't say if its good or not.
Oooh, now this is something. Will definitely consider this one. Thanks!