I'm sorry to hear that that was your experience of the game. It was certainly my intention to make a game that provided a more flexibility than you found. I'm not quite sure I understand since everything you've expressed frustration with is either optional to engage with or has a find-your-own-fun setting, but games are subjective, and you had the experience you had.
Just in case I've misrepresented myself, when I say that my expectation was that players would be comfortable destroying cells to make specific upgrades when needed, I'm thinking "destroy one or two cells when that's all that's in the way of making an upgrade," not "remodel the entire hive." The world is big - there's plenty of room to expand and build upgraded cells without destroying anything if a player thinks they need them (with the exception of a single upgraded Workshop, no upgraded cells are necessary for comfortably meeting the Jelly goal in time, though I'd usually recommend upgrading the Throne Room since the Activity screen can be helpful for monitoring role productivity).
To clarify, the default Queen's lifespan is 2 hours, and the cooldown before a new Queen can be spawned is 1 hour without upgrades (which was tuned to enforce a maximum concurrent Queen count since it can take much, much less than that to make the Jelly required for a new Queen). Some players have mistaken the cooldown on spawning a new Queen for the current Queen's lifespan, but when that expires it becomes apparent pretty quickly that the Queen isn't dead, and there's a warning event prior to the Queen actually dying to remind players to spawn a new Queen so they won't forget.
As I said, upgrades aren't "hidden" to create engagement - they're revealed when the player has earned them as a way of keeping things from being overwhelming in the early game first and foremost (some of this was driven by tester feedback during development), and secondarily as a new layer of construction concerns for players to consider (or ignore) for their subsequent Queens' hives. The "skip Beepedia locks" find-your-own-fun option lets players see (among other things) upgraded cell layouts in the Beepedia before they're researched, and for anybody keen to have a "second hive" type experience for a lineage's first hive, there's the "skip research" find-your-own-fun option.
From the pre-release playtesting I did, most fresh players were able to make the Jelly goal on their first attempt (even when Old Bitey paid a visit or two - he's a random disaster, and isn't guaranteed to make an appearance). Those that didn't were close, and generally chose to keep playing after their Queen died ("losing" is optional in Hive Time).
I added the "skip disasters" find-your-own-fun option in the Hiveversary Update, so Old Bitey himself is optional at this point too.