I'm glad that you enjoyed Isostasy!
You found a good Flobby! the glitched out cat enemy is 100% intentional. it's an easter egg. he just wants belly rubs.
I appreciate your comments about the amount of enemy HP as you play through the game. Yes, you almost certainly did miss upgrades. The fact that enemies become almost unkillable is supposed to be the hint to the player that you missed stuff and should go back and explore more. I think this is just a difference of opinion in style. when I play an open world game, I tend to progress slowly, checking in every nook and cranny before going forward. When I reach a new area, or find a new item, I tend to take that as a signal that I should go back and make sure I haven't missed anything before progressing (slowly and methodically). The game is designed to make you backtrack through areas you've already played through. Seeing and hearing how OTHER people play my game has really opened my eyes to the fact that not everybody plays that way, or enjoys that type of layout. This game's map is already done, but if I design any more games in the future, I will learn from that lesson.
Also regarding fast travel back to earlier areas.... well, explore a little more! (and talk to the sages!)