He doesn't do development himself(he does review everything before it goes into the production branch), simply that he knows better developers than I.
I have re-written much of our original code to a point where it is of good quality, both in it's intended role and in readability.
I did have a habit of cutting corners which later came back to bite us but that is not the case anymore.
I shouldn't judge from a piecemeal HN post. But the picture I'm getting is "Know-it-all Javatecht VP of Enterprise AbstractFactoryCorporateWarfareObject Development."
Here's some news: there's no such thing as a CTO (or for that matter, CEO) in a four-perspn company. It's cargo-cult status-seeking: the CTO of $BIG_CORPORATE where I used to work was rich and important, so I'll give myself the same title and I will be too. What's missed is that the actual status comes from having humans to boss around. So in a startup titles are basically equity: worthless until we're profitable.
Fire the CTO. He doesn't code, he's causing problems. If you really need him for his experience with "Enterprise-ready," hire him on a consulting basis for a few hours a week to tell you what to google. But if he's not coding...what is he doing?
Unless your are failing to get your code working there is almost no good reason to tell you to leave, this seems like some sort of power play. I would tread carefully if I were you. Even if they did decide it's better off without you "Expect to leave in 3-6 months" is a giant WTF? Why tell you now unless they are going to sweat you to give up equity. Telling you you aren't a good coder is a good way to get you to feel like your contribution to the company is less than it really is, but it sounds to me like you must have done all the work. Even if this CTO helped with the scope and guidance to get everything going better, what would they have if you took all your work and left with it? (Not saying you should try that, just realize how much of what is important did YOU actually create) Unless almost everything you've done is getting thrown out, you are probably undervaluing your contributions, from what you've said.
Good luck.
If true, that's beyond absurd.
HINT: This has nothing to do with your coding ability