1. Writing his own engine: This is an often discussed issue, but basically it boils down to 95% wasted resources. It's all time you should have been spending on a unique angle for your game, or a specific game-making gameplay feature etc.
2. Trying to create an RPG, JRPG or MMO: As a solo person these are highly problematic. The amount of roles you need to cover for these genres is ridiculous by yourself, which brings us to him outsourcing jobs because of the large art requirement.
3a. Spending $85k (Project 1) / $15k (Project 2): There was always only a very small chance to get $85k back except by going viral (such as with the Stardew/Undertale comment), which is in itself a very small fractional percentage chance. Aim for something reasonable such as $1k expenses for a first project. $10k is already too much and few projects will make that back. Spending more on project 2 than you made on project 1 is also an issue. Cut back as much as you can.
3b. Spending $4k on PAX (essentially advertising): As he himself discusses, he had no way to gauge the impact of going, but again it comes back to it being a really big $ amount for a first time indie developer.
4. Niche games are hit or miss out of the gate: Astral Traveler is the type of (Runner) game that doesn't promote word of mouth. They for example need some angle such as being extremely hard, pretty, controversial or competitive that will encourage people that they themselves need to give it a go, or watch someone else give it a playthrough. It comes back to asking what is the hook for the game?
5. Tech Support (His new/3rd Project): Gauging whether something will be a success is very very hard. At the very least he seems to have scaled down the costs, but on the other hand it doesn't look like an extremely interesting game at the moment. A big problem for indies is to find the correct scale of game. Too small and you're seen as a throwaway cash grab, too big and as an unknown that's not pushing the frontiers of the art you'll never make your money back.