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Last one!  That would be the victory points.

The goal being to prevent dragged out stalemate in the late game, while providing an alternative win condition.
   - seems pretty good on both of those accounts all considering.

The things to be enquired of course, would be if it felt like it made sense?  CD referred to it as gaining a 'critical mass' so that seems a good term, did that slow build up of advantage feel like becoming ultimately better capable of steamrolling the opponent?

Was the number 100 about suitable?  Admittedly, to win via army destruction would take 48 points, while structure booming is 50, making domination equivalent to double that as more passive.  Admittedly 100 was plucked out of thin air as it would ensure that a game would last at most 100 turns, and at least 11 if managed to capture everything straight off.  Which seemed reasonable.  Putting the points in line with the other victory conditions would be viable, but reckon that may make a few unlucky battles enough to be unsurmountable.
(An example being this round in that when Phyrexia managed to dominate all the planes, it would have won before the Coalition - all things constant.  Thus capable of overcoming being a little slower getting the places to start with)
   > that is not including army killing granting victory points, as that is more erratic and makes sense regarding resource advantage.

Happy enough with the numbers associated with army killing and domination of applicable planes however?
In the case of minor planes, it would likely be better to have just 1 victory point associated, if any.

If happy with how the simple version worked, it is viable to consider other things proposed by players when initially creating the system;
Victory points on occupation of enemy bases; the majority would need to be on destruction of course, but it would allow for more of the back and forth to contribute.  Can probably get awhile with 1/day without increasing the total needed to win.
Granting victory points for battles; not inclined to the more complicated underdog/circumstances variations personally, but attaching that to size bonuses (which considers rank and numbers jointly) could make it work.  A flat rate for victory/draw/not chickening out would be preferred.  Of course, that would need a higher victory point total (and each other component) to not trivialise other methods of victory - and have it not over within the first few turns!
Prefer to keep domination associated with terrain feature occupation so it can be seen at a glance.  But proportional armies has been raised in the past as well.  One matter would be that dominating all planes at once would not be possible until most things are dead - this could be a good or a bad thing.

My draft had something like this to say on victory

Winning a battle: 1 point, plus 1 point for each rank above the winner the loser was past the first (So a 1/1 army beating a 6/6 army scores 5 points).  If the underdog bonus seems too hard to claim that way, we could add a point for each rank worth of disparity, including the first (So a 1/1 army beating a 2/2 army scores 2 VP -- 1 for the win, 1 for the ranks).  If this would look to rack up VP too fast, we could leave out the VP for normal victory as well (So a 1/1 beating a 1/1 is no VP, but a 1/1 beating a 3/3 or 2/2 depending is 1VP)

Na-dip on both those accounts, righty-o.

Well, that is pretty much the full set of stuff available here, so it is up to thee lot if there is anything that could use changing, altering, or otherwise adding.  So post away for anything that strikes thy fancy, as with previous, if no get a seconding at the very least, then won't be incorporated into voting.  Otherwise, all good and fine.