I'd give the same advice I always give to indie devs - play it safe. So many games the dev want to add a feature or do something cool, underestimate how much work it is, and then its a year later and they're burnt out.
I think puzzles are a good idea for a lovecraft game. But I'd say keep them simple mechanically. Stuff like dialogue cues in convos having info to a question, branched choices for an important scene. The game in the church is about as complex as I'd go. And keep it limited to when its most important to have them.
Don't spend a bunch of time coding or trying to make a unique minigame, ui, etc. You can always add more to the game, more scenes, features, updated art/ui, etc after the game's main content is complete. Its a good idea to save any major coding projectings or overhauls until then and apply it to the next game.