Thanks for your kind words. I'm glad to hear that overall you enjoyed the game. Most of what you've noted is by design/with intent. If it's of value or interest, I'll give some insight/reasoning below.
With regards to upgrade patterns, I specifically didn't want new players to know or care about that stuff in the early game. My expectation was that most players would be content with destroying cells and remodel their hive to make specific upgrades where needed, and then use their experience/knowledge to inform how future generations' hives would be constructed when carrying forward past hives' research. Not everybody has embraced that though - I've found that destroying/repurposing cells is something that some people seem particularly resistant to, even though only 3 of the 8 non-storage cell types need additional space to be upgraded (since all storage upgrades use the same pattern, they can be viewed as one thing, I think). If that leads those players to make drastically different decisions for the layout of their second Queen's hive though, then I'm inclined to see that as a good thing since it surfaces more of the game's underlying shape/possibility space.
The longer term plan if I had the opportunity to continue to develop the game would have involved adding more upgrade options that used different patterns, which makes me a little reluctant to show a preview of the currently implemented upgrade options in case I ever do get to realise those plans. It's not something I'm giving specific attention to at this time, but if I come up with a way of indicating currently-unlocked upgrade patterns that would scale to show multiple patterns in a clear way, I'll definitely add it in a future patch.
The general design philosophy behind the role-specific management systems is that they should offer room for micromanagement for players who are into that, but also be optional and mostly ignorable for players who don't (eg: the Beesitter tutorial image shows a set-and-forget position for the population slider that will guarantee population growth). I've had some ideas for making Foraging management a little more elaborate (and what's in the game is a step beyond ), but I'm also keen to make sure it doesn't go too far beyond the other management systems' levels of complexity (it is currently the most complex).
Hive Time is very much not about bees, but it's worth noting that real honey bee deaths frequently occur away from the hive while out foraging/pollinating. It's sad, but from what I understand, less strain on the hive than when bees can't go out foraging due to weather and there's more dead that need to be disposed of.
Regarding the bear attack, I'm not sure what you mean by clumping security. Barracks placement doesn't affect the Bear Attack event. Defenders need to be deployed outside the hive to deal with external threats - there's an emergency button for overriding the slider and telling everybody to get out immediately if you hadn't spotted (though Bear Attack's lead time is longer than a bee's typical lifespan...).
Recovering from setbacks is a big part of the game in my mind, and my hope is that the first Bear Attack teaches players that it doesn't take much time or effort to rebuild. When I play for fun, I usually play without Defenders and just embrace Ol' Bitey and the wasps.