I don't know if you mean Nintendo developed, or published, but I'll just list a bunch of recent "Nintendo" games with playable female characters. The ones with a (?) are just Nintendo published (in NA, at least):
I omitted games with ambiguous characters, like Kirby and Yoshi.
Also, I left question marks off of some of the Camelot Mario sports titles, as they are ostensibly 'Nintendo' titles, even if not developed in-house. For no good reason, I left question marks on for Hyrule Warriors and Smash Bros. (mainly because they're in more unique predicaments than the Camelot Mario titles).
Let's see...
Splatoon - Great (female default)
Pokemon X and Y - Good (male default?)
Pokemon Omega Ruby and Alpha Sapphire - Good (male default?)
Animal Crossing: New Leaf - Great (no default, though super bad w/ race)
Animal Crossing: amiibo Festival - Great (no default?)
Animal Crossing: Happy Home Designer - Great (no default, race options)
Fire Emblem: Fates - Good (male default)
Fire Emblem: Awakening - Good (male default)
Super Mario 3D World - Goodish (multiple playable female characters, though one is locked until way later in the game; also main character is debatably Mario)
Captain Toad: Treasure Trackers - Great (Toadette is captured at first, but they turn the tables and have Toad get captured later and make her the lead; slightly problematic in that more levels have you play as Toad than Toadette)
Xenoblade Chronicles X - Good (not sure about default; didn't it come out that Elma was originally the star but was replaced by a gender-optional MC?)
Style Savvy: Trendsetters - Great (never played, but I presume it has plenty of female characters)
Donkey Kong Country: Tropical Freeze - Okay (as you note, Dixie is only truly playable in multi-player)
Code Name S.T.E.A.M. - Okay (main character is male, and the gender ratio is 6-3 in favor of men)
Pikmin 3 - Good (shares lead character credit, but I like her)
Mario Kart 7 - Okay (aside from Mii, only female character options are Peach, Daisy, Rosalina, and Honey Queen vs. objectively male characters Mario, Luigi, Yoshi, Bowser, DK, Toad, Wario, Metal Mario, and Shy Guy; subjectively male characters like Lakitu, Wiggler, and Koopa Troopa tend to be male by default when a gender is given, and when one is female, it's usually obvious)
Mario Kart 8 - Okay (the only original characters added from 7 to 8 are Toadette, Isabelle, Villager [who is male by default], and Wendy O. Koopa; most of the female character additions were different versions of existing characters, including Pink Gold Peach, Baby Peach, Baby Daisy, Baby Rosalina, and Cat Peach)
Mario Golf: World Tour - Okay (same issue as MK, most characters are male characters or generic enemies that usually default to male; without DLC, female players have only three choices in terms of female characters)
Mario Tennis Open - Poor (has a few playable female characters, but one of them is just Baby Peach; men meanwhile have 11 characters, with two generic enemies who default to male)
Mario Tennis: Ultra Smash - Okay (has better representation than Open did, significantly so; all female characters are original without any baby versions or whatever. It's 10 male characters, five female, and one generic)
Mario Party: Island Tour - Okay (2 out of 10 characters are female)
Fatal Frame: Maiden of Black Water - Great (haven't played it, but I am under the impression that it only stars a female character)
Super Smash Bros. for Nintendo 3DS and Wii U - Good (Significantly better than any Smash before it for representation. It still has MUCH more male characters, and many of the female characters are gender-option character. It does however at least have a gender-option character where female is the default)
Hyrule Warriors - Great (while Link is the de facto lead, there are a lot of female characters from which to choose, including a female main villain for the second time in the series' history if I recall correctly)
Fantasy Life - Good (not sure about default)
Yo-kai Watch - Good (as above)
Fossil Fighters: Frontier - Unsure
Bravely Default - Great (while the mainest character is male, the two female characters are great and are just about as important)
Bayonetta 2 - Great (for obvious reasons)
The Wonderful 101 - Okay (I like Wonder-Pink a lot, but she stands out as the "token girl")
Disney Magical World - Unsure
Puzzle & Dragons Z + Super Mario Bros. Edition - Unsure about P&DZ, and "Okay" for Mario (I believe that a lot of the characters, at least early on, are either generic enemies or Mario & Luigi)
Miis - A bit of a copout since Nintendo would actively have to be trying to be a jerk to not have playable female Miis but playable male Miis
I think with this list, the picture I get is that of all the games, only two -only- star a woman (Fatal Frame and Bayonetta). This is not to downplay games that have gender choices, but at the same time, you have so many games where the character is male, and that's your only choice.