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Glad my feedback was helpful! I'd be happy to offer you some further thoughts as well!

In its current state, the game could really go in a lot of different directions depending on the kind of vibe you're going for and different players will have different preferences when it comes to those different styles. I'd say it's probably a good idea to nail down the specific vibe you want to go for so future implementations are more motivated and less haphazard and disoriented. Personally, I prefer a more hands on incremental game, sort of something closer to an rpg style incremental (which is what made me curious to check this out to begin with), but some people prefer to buy a bunch of upgrades for things and let the game automate itself, which lends itself to a more idle approach.

For suggestions/ideas, I think if you want to go for the more rpg style route, having the materials atually mean something beyond a currency for upgrades would go a long way to achieving that kind of vibe. Like, there's currently no reason for timber to be timber, or ore to be ore aside from saying "this is the currency you use to upgrade this skill". There's no reason why that can't work if that's what you're going for, but I think if you wanted it to feel more intentional, then having a use for those materials that actually correlates to what they are would go a long way in doing that (eg. using the ore to make gear or something). This could also be used for integrating the skills together like I mentioned in my previous comment, like using the timber to upgrade supports in the mines to avoid collapses or something. 

Are the boss mechanics you're referring the guardian fights? (I'm not entirely sure, because there's nothing in the game labelled as being a boss and the guardian fights don't have any kind of difficulty curve that you generally get with boss fights) If that's what you mean then I'd say the direction you take that mechanic highly depends on the direction you take the rest of the game. If you introduce more skills, then you could definitely continue to have those fights be used to unlock the other skills (probably give them more levels though, and have the final level for each skill be the boss fight that unlocks it or something), but in its current form, having that be their only purpose makes them feel a bit redundant because there are so few skills to unlock, and unless I'm mistaken, defeating the fishing "boss" didn't really have any reward for doing so because there were no more skills to unlock.

Overall, I think a lot of the things you could do with this depend on whether you want this to be an incremental with minigames that's reskinned to look like an rpg (which is what I'd currently describe the game as, and you can lean into that more if that's what you're going for), or if you want to make an incremental rpg that actually has rpg elements to the gameplay itself beyond just the names of the items and stuff. Both are perfectly valid paths to take, it just depends on which one you're more interested in making. My suggestions were mostly based on the idea of going down the latter path because the vibe of the game lends itself well to that, but you can also keep the rpg elements purely aesthetic and focus on improving the incremental elements instead if that's what you want to do.

Sorry if this was a bit long-winded or repetitive, hopefully it gives you some food for thought though. And good luck with the game!