Lots of good answers here, but I’ll add some gay to the mix as well:

• Cherry Magic, a story about the need to know others and the vulnerability of being known with a strong emphasis on healthy communication.
• Given (first season ONLY), a story about healing from trauma and letting out difficult emotions via art. The anime very cleanly divides the somewhat fraught manga between the actual cute and wholesome (though often sad) story of the high schoolers in season 1, and the extremely unwholesome and honestly kind of disgusting messy drama of the university-aged bandmates in the movie, so I’d suggest just watching the tv anime and pretending the story is over.
• Sasaki & Miyano - just a cute little fluff anime. light on substance, but so sweet.

I’ll also second My Dress-Up Darling* and A Sign of Affection and add My Happy Marriage, Snow White with the Red Hair, and Recovery of an MMO Junkie

*depending on how you define “wholesome”. I know some people would require it to be chaste, which dress-up darling is very much not, lol. IMO, the story uses sexuality to inform and develop the characters and their relationship and does so in a very wholesome way.