So, to recap again:
1. During the upkeep phase, you decide the order of events that affect objects that you control.
For example, If your opponent's Ghoul Rot is damaging your creature, you decide, not your opponent.
2. During the upkeep phase, if an event should occur, but it would affect objects controlled by multiple players, the player with Initiative decides when it happens.
For example, if Death Link will heal you and damage your opponent's enchanted creature, the player with Initiative decides when to do that.
3. The exact wording of an ability matters. Highland Unicorn gives all creatures the Regenerate 1 trait, so each healing is a separate event, and will happen sequentially. But the 8th skull on Altar of Skulls gives all creatures the Finite Life trait, so it only happens once, not to each creature individually.
4. For a single event in the upkeep that affects multiple objects with seperate controllers, the player with Initiative derermines when the event happens, as if they controlled each affected object.
5. During the upkeep phase, the player with the initiative also determines which player to ask "what happens next?" The chosen player can only answer with events that affect an object they control, as usual.
6. The player with the Initiative may of course choose themselves to pick the next event. And they also are the player that choses the time of occurence for events that affect multiple players's objects. The combined effect of these rules is that for these sorts of events, the player with Initiative choses exactly when the event happens.
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Outside the upkeep phase, RAW is that the player with Initiative resolves any timing isues by going first. I concur in part and dissent in part with Zuberi on this one.
I disagree that this isn't a playable RAW. If I have the Initiative and three events that could happen, and my opponent has four, what happens first? The rules say that I "go first," since I have the Initiative. There's no way to reason that away, without declaring a rules error, which I don't see enough evidence for, yet.
Ok, so if I'm not ready to declare a clear rules error it's incumbent on me to explain how exactly we can play the rules as written. Do we take turns or something? Nope.
After having my go, now I have two events and my opponent has four. As happened before, I go first, because I have the Initiative. Then, yet again, there is a timing issue, and I go first. Finally, there is no more timing issue, and the other player acts.
This is exactly what happens in the Upkeep phase except that instead of giving the player with Initiative a choice of player, the rules chose the player for us.
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So, uh, are there any other reasons this might be a rules error?
Well, yes. The biggest problem is that I can't find any card this rule would apply to. Zone attacks would be the obvious candidate, but the rules specifically say that in their case the attacker choses the order.
How about Force Wave?
http://forum.arcanewonders.com/index.php?topic=13953.msg34022#msg34022 Nope. It's an old ruling, and not justified in writing, but the decision is that the Caster chooses. It's that way in the FAQ, too. Same for Repulse. Same for Gate to Hell. Same for Earthquake.
In fact, I can't find any example where the rulebook is even cited for this sort of question.
So the rule, in actual practice, is that the controller of the spell gets to pick.
I don't know how we got into this situation, but that's the answer. I propose altering the Codex and FAQ to reflect it.