Well-written male characters in anime are exceptionally rare.

I think 3gatsu no Lion is my first thought. The main character is done well to the point that it feels almost obviously on a different level from 99% of other anime.

Other thoughts:

• Gurren Lagann: Kamina, Simon, and especially Rossiu in the second half.
• Toradora!: Ryuuji. Especially his relationship with his mother and grandparents near the end of the show.
• Monogatari Series: Koyomi. I’m really thinking of Owarimonogatari here. Ougi Formula and the next couple arcs. He’s pretty simple before then but Owari is really spectacular with his characterization.
• Maison Ikkoku: Godai is one of the best male protagonists ever. He’s not likeable at first, but he makes so many microscopic improvements throughout the show that he feels totally different by the end.

Also: Neon Genesis Evaluation, 5 Centimeters Per Second, Christmas in January, FLCL, Infinite Ryvius, Ocean Waves, Mob Psycho, Working!, and probably Made in Abyss.

Ouran High School Host Club gets my vote for worst-written male characters, excepting of course Haruhi’s dad