Why do the Wither Storm's Tractor Beams enrage Endermen so they attack it? They're fired from its eyes, and an Enderman's Berserk Button is being looked in the eyes!
Axel is an Griefer who wears green and is first introduced when he is wearing a Creeper mask. Lukas starts off as a Lovable Coward but can become Jesse's most loyal friend if Jesse treats him well; he is first introduced from the back which shows off the Ocelot head on his jacket. If you know how well Creepers and Ocelots get along in Minecraft then is it any surprise that Axel and Lukas have problems cooperating?
When Soren is telling Jesse about The Order's battle with the Ender Dragon, Ivor—who we established a few chapters ago was a member of the Order back then—is the only one to not play any role in the battle. Why? The story was fake, and Ivor was the only one not cool with this fact. Since they had to have come up with the cover story before Ivor departed from the Order of the Stone (otherwise he wouldn't have known about it to turn it into the final puzzle), Ivor probably decided he wanted nothing to do with that lie and requested to be left out of that particular legend.
A major theme in Season 1 is how legends and stories can become altered with time, and how the Order of the Stone deliberately altered their legend to make them sound better than they were. The very first choice you make in Season 2 is whether or not to let Lucas embellish the New Order's legends in his book. If you do, you're falling into the same trap of fame over integrity as the Old Order. However, if you insist of the events being told as they happened and no more than that, since Lucas can give a first (or at least second)-hand account of the events of the previous season, if that book is published, a solid, unabridged source of the New Order's legend will always exist ahead of any altered retellings.
Why does Season 2 have a stamina meter in combat but Season 1 didn't? In the 5-7 years they've been running Beacontown more than they've been adventuring, Jesse's probably gotten a bit out of shape. Seems Petra wasn't too far off the mark after all when she thought Jesse was getting rusty.
Why did Aiden and company become far worse in Season 1 Episode 5 than he was prior? Because Lukas left(or was kicked out). Recall that, throughout Episode 1, he was often the one to rein in the Ocelots' taunting of Jessie and company. Without him, the "Blaze Rods" as they now call themselves have no Morality Chain to keep them in check. Though this comes with the fridge horror that Aiden was always that deranged, deep down, and we just never saw much of it because Lukas always stopped him from going too far.
We're never told why exactly Hadrian and his cronies want the Redstone Heart so badly, but if it could power something like PAMA, they could be planning to power something less well-intentioned with it, given their nature.
The disc playing on Soren's radio ("Redstone Baby Doll") sounds like a wistful love song, 1930s-1940s style. Soren's Enderman song is upbeat, but also has a wistfulness to it. During the Episode 3 credits, both songs play. In Episode 3, either Magnus or Ellegarde die. Going by what Soren told Ellegarde before she died made it seem like the love song was sung by him to her, and the Enderman song is a farewell song to friends. No other names besides "Gary" and "Sally" are mentioned as the names Soren gave two Endermen, but it makes one wonder if he named four others after his Order friends.