You bring up really great points! The first, regarding the use of headers, was something that I did think of, but decided against. One problem I had with the usage of headers was the fact that I felt it's too sharp of a context switch while you read the article. While it does allow for newcomers to quickly glance over the content, I felt that it would be better to prioritize the reader that already took the time to read. I tried to make the concept to concept flow as clean as possible. Instead of headers, I wanted to use the images as a way to naturally delimit the content as you read, without breaking your attention.
I'm definitely not sure that what I chose to do is the best way forward! This is actually the first piece of writing I've really released or had anyone other than myself read.
Regarding the second, it was definitely brought up to me it would be interesting to bring more detailed comparisons into the mix! I did a little bit of it with the mention of rogue likes and the Supergiant games. One thing I'm still working on is balancing the content so that it doesn't detract too much from the Cave Story - at the end of the day, the article was meant to be a tribute to the hard work put into the game by its creator, and the amazing qualities of video games.
This was very hastily typed up (I'm actually traveling at the moment), so hopefully my intentions and logic behind the writing makes sense! I definitely plan on thinking more about the points you've brought up to incorporate into my writing in the future, so thank you SO MUCH for the honest feedback!