Thanks a lot for the feedback!
1. Yeah, that one is genuinely annoying. Maybe we didn't put enough polish into it, so I'll take another look. The issue is that before, the first items merged into seeds way too easily, which was unbearable. Maybe we could make merging more lenient except for certain items, or add a setting that allows more lenient merging for players like you who find it frustrating. We'll think it over.
2. More automation is definitely planned.
3. We already have chests! But right now it's not clear how to get them, so we'll add a quest for that. I'd also like houses to give a capacity bonus, so it feels more like you're actually building a village ^^
4. I completely agree, that's also something we're planning to do.