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I'm stuck after getting the first upgrade (legs). I can't figure out how to get to the destination on the map. The red section is blocked and I can't progress any further right than the screen where you get the legs. Is there something I'm missing about the legs that would allow me to walk through a one-tile-high space?

After getting the legs, your next destionation should be in the top-left corner area (purple). If you found an indicator for the red area, I might've placed the indicator item for that badly.

Okay, made it to the purple area, but I can't figure out how to progress. Got a few coins, but I can't figure out how to go beyond the teleporter or above the central column.

I feel this would be better as a linear puzzle game instead of a Metroidvania. I discussed this when I reviewed Antichamber, a game that did a similar thing: A Metroidvania is based around seeing a barrier and recognizing you can't pass it until later, but puzzle games, by their nature, obscure whether you lack a necessary upgrade or just aren't smart enough to figure out the puzzle; the question of whether you can pass the barrier isn't obvious. This potentially leads players to ignore solvable puzzles because they think they lack the means to solve it while futilely bashing their head against a puzzle that is impossible.

The only "Puzzle Metroidvania" I've seen successfully pull this off is Toki Tori 2, which did it by having no formal Metroidvania upgrades or hard barriers; the only barrier to going off the beaten path is your ignorance of the puzzle mechanics. But if you're replaying the game or are very clever, you can sequence break anywhere you like.

Have you played La Mulana 1 +2 or Environmental Station Alpha?  Those are some of the best games ever made imo and are puzzle metroidvanias.  Puzzles in metroidvanias can often double as "secrets" which really makes things interesting- especially when they involve lore, world structure, or map knowledge as a part of the the puzzle.  

ESA is a very straightforward Metroidvania. The only "puzzle" aspects are in the endgame. For La-Mulana, its puzzles are largely disconnected from its ability/item upgrades, so they don't have this problem.