On this site, I'd have to say the best written MC is Haruhiro from Grimgar. I also liked NeeChuu's MC, it was a riot to read him suffering through his sister antics. There's also Dendrogram, Ray is a really compelling character.
On Non-JNC LNs, I'd say Kazuma from KonoSuba. Godou in Campione also had a really great development throughout the series, it never received an official release though, thankfully it's fully fan-translated. Also Taimadou Gakuen's MC, though it received the same treatment translation-wise.
On normal western novels, the list would be too long so spare me from that lol.