Okay, while FE Gaiden holds the spot as the first Zelda 2 for FE, I'm willing to bet FE Fates could be called the second one.
First, by Zelda 2, I still mean good game, but that it will always be considered a black sheep when compared to its predecessor unless you share my opinion about FE Gaiden due to unusual design choices and fixing problems that weren't broken in the first place. See weapon durability and the weapon triangle, hot springs, and FE Amie
It's no secret to say FE Awakening revived the series, and just like in Zelda 2, the decision for the sequel was to change the formula completely. We now have paid route splits, a completely revamped weapon triangle, and new weapon mechanics overall.
Also of note, a large majority of mechanics seem to be taken from FE Gaiden the first FE Zelda 2 and improved upon see My Castle and weapon system. In conclusion, FE Fates is FE's second Zelda 2.