In my experience the hardest thing facing a CTO is the very nature of the ever-changing world of web applications. In other words, stuff changes real fast!
We started prototyping an MVP back in November 2015, and now since we've been looking to pivot, we've found that we're approaching our stack very differently. Frameworks have been updated, some drastically, some open source software we used is now deprecated and non-supported, other software we built our app upon has shown to not be scalable enough, and so on.
One has to just make a decision to commit to their stack and work with it, or (if absolutely necessary) make sure that the application you are building is built in such a way that you can still take it apart and put it back together again on a different stack – which we did actually.
For me personally, I like to make sure that the application is well documented from the beginning and designed first on paper (or online sketches), with a database structure clearly defined, routes documented, and the flow of the user experienced explained in human-readable text. If that is done well, then changes to the stack will have a lesser impact on the path to your MVP.
