Good question! This is a really interesting observation to bring forth and I think that there could be a multitude of reasons why your stories featuring him as the main character might not be performing as well.
One thing to consider, is how comfortable you are writing in the "voice" of a character. This is especially tricky when you get into fandoms that have several reboots of the characters, and they all have their quirks that make their "voice" different. If you struggle to get into the head of a character, it may show in your writing. Personally I have to really focus when I write Master Splinter. It isn't easy to write characters we struggle with, but practice and studying the character from the show might help with this.
Another thing to look at, is whether or not people are expecting a certain "kind" of Mikey. Someone who believes Mikey is a shallow goofball who pranks everyone, might not respond well to a writer's version of Mikey that is serious, or insecure. This isn't wrong for either of you since you both are interpreting a character how you see fit, but you won't be able to please everyone if that is the case.
I have also noticed that Mikey as a character has a weird relationship with fans. There are people like me and Zelgadiss who love the character, and will write him frequently. But he also isn't quite as popular as Don in stories that I've seen (as a main character). I don't think it is Mikey fans not being invested in the fandom, but just less representation. He isn't an easy character to write and I'm not sure about drawing (not an artist in that way) and I know of others who struggle with portraying him, so they decide not to.
I think that it is always possible to improve writing, whether that is grammar, character portrayal, or plot development. Practice is vital for getting better, and checking in with others like this is a great resource. I think it might help to define how you view the character. Watch the show that you think portrays him best. Read other Mikey fics that you really like and analyze why you liked them. Start building a strong foundation for your character that you can draw from when placing them in situations in your fic.
Now please note these are my own observations and opinions. However, I think you are a great writer, not only for your work but for trying to improve. That is awesome, and I look forward to seeing what you come up with!