So in my last game I turtled a little, and when the Collaboration or Catclysm quest popped up, I decided I was finally going to complete it this time.

I did not. Because like in almost every single game, when I had finally found all the lodestone systems, I had two choices:

• a) unassign half my heroes from their planets, split my fleets, and park them half across the galaxy for at least ten turns hoping I would not be attacked or
• b) take those same fleets to the last home system not in my alliance and win the game in less than five turns

The rewards for completin the quest are significant, but no reward is significant enough if the quest takes far more ressources and time than winning the game.

Of course in my case the AI had also cunningly parked a single colonizer on one system just after signing a truce, preventing completion for everyone. In the spirit of reducing the tediousness of this quest, could we remove a few of the arbitrary restrictions? Currently, the quest feels less like "fighting the other empires for control of the system" than "fighting the arbitrary ruleset to finally get to see that cutscene".

• lower the time needed to be spent on a single system to 5 turns or less. I think the case where someone can hold a system for five turns, but not ten, is rare at this point of the game.
• remove the hero requirement, it just seems arbitrary. You need to contest with a strong fleet either way thanks to the auto spawns of the opposite team, but this would remove at least the annoyance of having to unassign half your heroes to complete the quest in a humane time limit. Maybe just start with a strong neutral fleet spawned in each system which either contester has to defeat.
• Merge part 1 and 2 in one, i.e. you can start the system ticker as soon as you find the system. I assume the split is to give everyone a more equal chance to contest, but to me the larger problem is the ruleset drawing the quest out long after the game is effectively over, even on endless difficulty.

To me, the quest would be a lot more fun if it were of the form "defeat initial barrier, hold for a short while and defeat possible contenders, move on" instead of "have all of your fleet and heroes sit nowhere doing nothing for half an eternity to satisfy the ruleset"

What are your thoughts on this? Do you usually complete this quest?

Yeah, I've been complaining about the said quest a lot too and pretty much never complete it, unless I intentionally delay my victory. Other issues are 

• The quest fires too late in comparison to victory conditions, though I think that's more of a general issue with all victory types being achievable too early in general. In a 300 turn game it's very easy to achieve any non-militaristic victory well before turn 150, the supposed mid-point of a match. Hence I think the victory conditions need a rebalance rather than making the quest itself fire earlier than it currently does, so the quest rewards (and all the other other last tier tech for that matter) have some time to stay relevant.

• Another problem is that the quest doesn't end when one side conquers over half the required systems (f.ex. 5/9 or more), which is kind of silly since the losing side can't win anymore at that point and gameplay wise there's no reason to fight over the remaining ones. The devs however are apparently aware of the issue so we may get a fix for it at some point.

I personally don't mind the hero requirement since I think it's a gameplay decision to spend time on leveling admirals rather than governors, both for normal war and in preparation for the final Academy quest, though I guess the capturing part itself could be faster and the AI should be more active in doing it as well.

One possible fix for "fighting against the rules" when it comes to quest and diplomacy is making the quest systems no man's land so you could enter and attack in them regardless of current diplomatic relations. I personally also think that only the opposite side's heroes (rather than any ship) should be able to contest and halt the other team's heroes' Lodestone system capture progression, in order to prevent the issue like you had with the enemy colonizer or other kind of rule abuse by throwing 1CP trash fleets to make enemy consume their action points.

I'm not participating in the new mystery beta, but hopefully the upcoming content has some fixes for this quest as well.