I can't think of any series that actually did almost **** up but managed to bounce back, but I can think of a few that personally did for me.
First the obvious one, Zelda. The whole era after Wind Waker and before BOTW was kind of a dark era for me. None of the games were bad, mind you, but that era definitely has my least favorite zelda games.
SS and TP are my least and second least favorite 3D zeldas, De DS games speak for themselfs, and triforce heroes(and Skyward Sword) almost made me quit the series because I was starting to hate the direction the series went in. A Link Between Worlds is the exception and was a fantastic entry but that wasn't enough.
BOTW made me fall in love with the series all over again though.
Smash. Even for someone who plays Smash more casually like me, Melee was still the best gameplay wise. Brawls sheer content couldn't beat that, although I still enjoyed the heck out of that game. Smash 4 a bit less though. I didn't like most newcomers, the gameplay still wasn't there, and it didn't have any cool modes (except smash run stuck on the better 3ds version). Not a bad game and I still played it a lot with friends, but my least favorite smash so far. I had less and less hope for the new smash and hearing it might have been a smash 4 port didn't get my hopes up.
Ultimate however turned out to be my favorite smash now. It has the content I wanted, and the gameplay, although not as fast as melee, is still very good. I wish it had more single player modes but I'll settle with this.
Monster Hunter. Most (G rank) entries were some of my favorite games ever. Freedom Unite, 3 Ultimate, 4 Ultimate. All top notch games that any fan of the series should play. However, I really hated what they were doing with generations. The new monsters were okay, but I hated the styles and Hunter arts. While also trying to be an anniversary game, (something 4U did way better) it also removed the soul of the series. No cool monster cutscenes, removed the story, terrible quest progression, terrible deviants both in design and fights, loaded with AOE attacks straight out of Monster hunter Frontier, ruined the fight of lagiacrus, one of my favorite 3U monsters, terrible hyper gimmick, and removed the diva song from the credits for some loli idol song for pete's sakes.
the only thing I liked, playing as a cat, wasn't even really valid, unless you got a perfect boomerang cat which took a lot of RNG. Then Gen U came, which was just more of what I already disliked, so that made things even worse.
After Gen U I totally didn't expect them announcing Monster Hunter World, which basically fixed most issues I had with Gen/U. And now with the Iceborne expansion, its probably my favorite Monster Hunter title right now.
Basically my I got disappointed in my top 3 game series but they all 3 bounced back (kinda) recently.