I think that Time Eater is the most hated one because it's the most effective at hating out its chosen strategy.
I disagree with that statement. The Time Eater is just the most in your face about it. AND I think even in that case people don't fully understand what the Time Eater is hating out.
The Time Eater hates on playing a lot of "low impact" cards in general the way the Awakened One hates on "low impact" powers. I have decks all the time where I can play 12+ cards per turn and still easily beat the Time Eater. It doesn't hate those out at all. What it *does* do is give cards like Flash of Steel and relics like Unceasing Top an actual downside.
The Awakened One is mostly an endurance battle that also hates on "low impact" powers like Well-Laid Plans. It's the only one of the 3 bosses without any infinite scaling on the boss itself, but it has enough health (combined with voids and health regeneration) that most decks take several turns to kill it while also having to put up moderate levels of defense each turn.
Donu and Deca is a flat out damage race that is heavily resistant to low levels of weakness/vulnerability. This battle is meant to force you to have large amounts of vanilla damage and/or rewards having AOE damage and/or heavy poison significantly more than the other two fights. There are no "break" turns where the boss is guarding or only dealing 20 damage, and the boss you want to kill 2nd is also putting dazes into your deck, so you can't always just sit on your laurels and tank up like you can easily do with the other two bosses.
A huge part of TE's power is locked up in countering a deck type.
I don't agree with this either. The boss has an attack that does weakness/vulnerability (forget which right now) and draw reduction, a guard that does vulnerability/weakness (whatever the other one is), strength scaling off of the time warp effect and a multi-attack, and a mid battle healing purge. If he decides to skip guarding altogether and puts vulnerability on you early the battle usually only lasts 3-5 turns without massive amounts of block. And on the other end of the spectrum if he guards and puts weakness on you a lot the battle can easily drag out to the point where the strength scaling gets really out of control. The reason I made the post complaining about this boss is that he has the ability to be faster than Donu and Deca or tankier than the Awakened One, depending on what he decides to do, on top of the already annoying Time Warp effect. And it's easily the least predictable of any of the boss fights b/c (I do agree with this part) the fight has such a massive spread on how it's going to go depending on RNG. This is the only one of the three fights that makes me worry about taking Runic Dome at the end of act 2.