Have you seen Ittle Dew? It's a puzzle game styled after Link to the Past. Female protagonist, cute, funny, difficulty ranging from easy at the start to maddening in the bonus areas.
Ittle Dew is a game I appreciate for having two generic characters that just happen to be female without it being anything important. While the human is identifiably female without being feminized, the magic animal sidekick could easily be male with no change. There are only two short lines of easily-missed dialogue where the two characters say "wait, you're a girl?" about the other.
Beyond that, there's nothing that brings gender at all into it when a lesser game would have made a running gag about the main character being a "tomboy".
It's not a major victory for feminism or anything, but I think we need more generalized characters that just happen to be female to get over the idea of femaleness being something that has to be pointed out as a defining trait.
Ittle Dew and Ittle Dew 2 are neat lil' Zelda clones with fun characters and much more emphasis on the puzzle aspect. Some of these get surprisingly tough.
Honestly, most Ludocity games could go here, including Iji, which is an indie 2D-shooter/platformer that did the whole "pacifist/kill everything" gimmick before Undertale, and is completely free to play. There's also a shitton of replayability in general. I'm surprised it doesn't get talked about more, honestly.