I think we have two choices: one obvious and one definite fan-favorite. (Btw, in case of people who haven't watched the latest episodes: SPOILER alert coming!)
The obvious one is the Moon people. With the Moon people being lied to by their leader, and Donald most likely as their prisoner, we might see an invasion of sorts coming.
And the fan-favorite one? One word: ... Negaduck.
Honestly, if they treat this character right, he could be a WAY bigger threat than the Moon people starting a war. Why, Neggy could easily use his charisma and new-found ruthlessness to take down Lunaris and gain a personal army for... well, taking over the world seems big enough to satisfy his ego.
OK it is exciting that the Big Boss is none other than F.O.W.L., and it's even more exciting that the head of F.O.W.L. is none other than Scrooge's Board of Directors (I never liked those guys, especially when they had Scrooge stopped looking for Della) (and you know, that would make perfect sense, since Scrooge was once recruited by S.H.U.S.H. to help Beakly stop Black Heron, and you know count think of it, that would explain even more of having Professor Ludwig Von Drake in the next season, since in this version of DuckTales, he's the head of S.H.U.S.H.) but I hope they do have Solego be the Final Big Boss in the SERIES finale, you know now that I think of it, like Bill Cipher and the Evil Entity in the series finales of Gravity Falls and Scooby-Doo: Mystery Incorporated
Now that I've watched the season two finale, I can start theorizing about the "big boss" of the next season's finale.
I've seen quite a few comments here suggesting Solego as a major baddie. Since we've seen the artwork of characters from quite a few Disney Afternoon shows (Gadget, Kit, Molly, Goof Troop -style Goofy, Gosalyn), and how the Solego storyline in the comics used those show's settings together... well, it might not be such a far-fetched theory. Maybe if the show's popularity leads to, like, season four.
However, with knowledge about the ranks of F.O.W.L., I'd say season three might have at least three episodes focusing more on Darkwing Duck and his enemies: we've seen the artwork of Taurus Bulba and just got to see Steelbeak in a cameo. And since Magica De Spell has already co-operated with him in the comics, we might see Negaduck forming this show's version of the Fearsome Five...