Not seeing Transistor but if you want a female protagonist that will make you cry your eyes out at the end, I recommend her.

Games As Literature 101 has a documentary that goes into a deep dive about Red as a character.

Also some people used Red's song from Transistor as a wedding song 😃

The modern tomb raiders are pretty decent.

If you're into the anime aesthetic: Nier Automata, Atelier series, and Recettear. I think FFXIII is fun but people would argue otherwise.

The tomb raider Trilogie

Here's one a ton of people slept on, Disciples Liberation. The protagonist is a chick, you can be pious, kind, hateful, evil and/or fuck your way through the entire world if you want. You can be bi, straight, not get involved in romance at all, doesn't matter. But no matter how you play, you are an absolute badass that can barely beat two soldiers at the start and can nuke literal gods by the end.

The Mass Effect series is still my favorite, you can choose your protagonist to be female and the game will adapt accordingly. Or Dragon Age if you are more into fantasy.

Chorus is a space dogfighting game that's quite fun. Has good storytelling. Doesn't pad time with repetitive/recycled quests so progression always feels unique. Some people find the inner monologue of the protagonist annoying but it's fine imo

Great lists already. I'll add What Remains of Edith Finch

Good is an incredibly subjective term. May be you can try Control. Or, if you're into rythm games and metal, I'd recommend Metal: Hellsinger.

Echo

Ms. Pac-Man https://en.wikipedia.org/wiki/Ms._Pac-Man

The only game that comes to my mind now that hasn't been mentioned yet, would be Tchia. Very sweet game.

Skullgirls!

The Great Giana Sisters!

Pokemon, anything equal or newer than crystal.

I just started playing Asscreed Odyssey last week, having fun so far. A bit of a departure for the series, more of a Witcher-style open world action-adventure game in ancient Greece. You can select between player characters Alexios (male) and Kassandra (female), I picked Kassandra, I like her, she seems decently written and the voice acting is great.

Elden Ring is incredible, although it's silent protagonist (aside from grunts etc), and might be too difficult. I know many women who love it though.

CrossCode is an excellent neo-retro overhead 2D action RPG. Great combat system, puzzles, and story.

Valheim isn't very story heavy but it's an incredible exploration/survival/crafting game, one of my all time favourites.

Steve Jackson's Sorcery! Parts 1 & 2 (and sequels Part 3 and Part 4): Masterfully crafted interactive "choose your own adventure" videogame, pretty much a video-book with an immersive story and wonderful illustrations. Highly recommended, I've been enjoying Jerma985's streams of it. You're constantly making choices that will completely change the outcome of the game, there is a rewind button if you need it.

Control has already been mentioned by others, I also recommend it. Great writing, graphics, lots of humour in the environment. Especially if you're a fan of SCP. Honestly the combat got a little monotonous towards the end but it didn't overstay its welcome. The documents you find around the world are hilarious and well worth a read.

Play Sea of Thieves as a female.

Soul Hackers 2 is a nice little palette cleanser of an RPG. Not as expansive as other Megaten games but it kept me engaged all the way through. The main party are all adults too which is a nice change of pace.

Alba is a very cute and relaxing game, but it's good! And the eponymous main character is a little girl.