Hey, thank you for the feedback! In terms of adding puzzles and exploration - some things just wouldn't fit in the current style of the game, since it's based on replayability whereas puzzles are only interesting the first time you solve them and become tedious afterwards. Surely, something could be done in this regard, especially to improve exploration, but it's not as simple as it might first seem.
As for being able to influence the parts you receive, this is something that could be addressed once we have a little bit more parts. We don't want players to get the perfect build every time, we'd rather you guys and gals work with what you've got and make creative use of your current situation. When more zooids become available we could allow to slightly influence the RNG in one way or another, but not too much. There is also the idea of adding a sandbox mode where people could just go nuts with whatever designs they could think of. The non-linear hub idea is interesting, but it would require us to tailor all of the levels to scale according to the players' progress. If the levels stay the same, the challenge would become a bit of a grind, though it does have the benefit of allowing everyone to advance at their own pace.
We're working really hard to get Sipho ready for release and we hope that with time we can make the game bigger and better. Thank you again for all the feedback and ideas :)