Yeah, okay. Let's look at the best selling games in Japan for the past few years and examine the male characters.
1. Monster Hunter X (3DS)
The one on the left is an example of male armor. Not seeing anything there that makes them look like little girls yet, but there's still time!
2. Yokai Watch Busters (3DS)
They are dressed like Ghostbusters, which are now women, so you have a point here I guess!
3. Animal Crossing: Happy Home Designer (3DS)
Now we're getting to Nintendo stuff, so clearly this should fit your point!
4. Splatoon (Wii U)
They do look similar in that they're both pre-pubescent, so technically correct!
5. Dragon Quest VIII (3DS)
Looks like a girl in that Toriyama can only really draw one face, so technically correct again! Man you are on a roll.
Let's just do a list of the top ten of 2014.
Yokai Watch 2: Ganso/Honke (3DS) 3,050,178
Pokemon Omega Ruby/Alpha Sapphire (3DS) 2,464,850
Monster Hunter 4 Ultimate (3DS) 2,381,177
Super Smash Bros (3DS) 2,066,022
Yokai Watch 2: Shin Uchi (3DS) 2,007,327
Yokai Watch (3DS) 994,346 / 1.280.799
Mario Kart 8 (Wii U) 842,053
Dragon Quest Monster 2: Iru to Ruka no Fushigi na Fushigi na Kagi (3DS) 748,139
Kirby Triple Deluxe (3DS) 687,957
Super Smash Bros (Wii U) 478,366
Weird, I am not seeing this overwhelming trend you are talking about. I think when you say "most Japanese" games, you mean FFXV, Star Ocean, and Ni no Kuni 2, and only the latter really counts. Persona 5's main character looks mousey, but not like a little girl certainly. Dark Souls 3 is a create-a-character. MGSV starred Big Boss.
If you're talking about, like, Idea Factory games, then that is a SUPER WEIRD AND NICHE pull to pretend it is a trend influencing Zelda.