All four Syberia games
Resident Evil Code Veronica, Zero, and both Revelations games (Claire and Jill both have equal billing with Chris and Barry in their games and same with Rebecca and Billy in Zero)
Bloodstained: Ritual of the Night
Eternal Darkness: Sanity's Requiem (Most of the playable characters are men but Alex is the main protagonist.)
Castlevania: Order of Ecclesia
Battle Chef Brigade
The Shantae series
The Blackwell games
Broken Sword 2
Detention
You forgot two of Kenji Eno's other games, D2 and Enemy Zero
Heaven's Vault
JULIA: Among the Stars
The Nelly Cootalot games
Paradise Killer
The Procession to Calvary
Spiritfarer
A Short Hike
Technobabylon
Sylvio
Whispers of a Machine
Unreal (The FPS)
What Remains of Edith Finch

@ZapRowsdower Thank you for the recommendations!

Cross Code, and Raji: An Ancient Epic both come to mind.
I don't believe there's a single Touhou game with a male protagonist, though you should probably do what you did with Metroid and just have one game represent the whole franchise
Wild Guns Reloaded may count by your rules. 2/4 characters are female, and you stick with one character till the end of the game. No character gets more or less content then the other.

Yumme Nikki
Demon Turf (and its side game)
Soul Hackers

Oh my apologies. I meant 'Soul Hackers 2'.

But now that I think about it, for Soul Hackers 1 the main protagonist, who is male, is a silent protagonist. The main female character gets a ton of focus, participates in every fight, has lots of dialouge and personality, a notable story arc, and so forth. So yeah, she isn't the "main playable" character but I believe she still qualifies for this list. She's on the cover art even.

Just sorry about the mistake earlier, Soul Hackers 2 unmistakably stars a female protagonist.

@AlphaOne2 Thanks for the correction

Princess Farmer & Ikenfell!

A Hat in Time

Another Code/Trace Memory has a female protagonist! Also Grimm's Hollow and Nights of Azure :)