For example, the 1v1 ladder has an issue where people who're good lose a lot of games by boot when real life happens and suddenly inflate a lot of rankings

Since when has this been a big issue in the 1v1 ladder? This is the first time I have heard anyone say that this is a problem with the 1v1 ladder system.
Also if real life happens the good players will either quickly put themselves onto vacation mode if they have some time, if not then whatever happened was much more important than a rank on a ladder on a game, so I don't really see the problem.
It's like saying a major flaw with real-time games (including the ladder) is that people can't play for as long as they expected and they get booted

Edited 10/29/2015 16:39:02

If a player is behind on armies and income by a significant amount and they've been the one holding up the game, a pairing penalty could be applied to the one behind and a pairing bump for the player that's ahead. It wouldn't change current ratings or rankings, but might improve paring.

^You could do that, yes. Not sure the exact formula, but that could be done.

Since when has this been a big issue in the 1v1 ladder? This is the first time I have heard anyone say that this is a problem with the 1v1 ladder system.

For players ranked 100 and below, check their biggest wins (the thing in the top right corner). A good portion of them tend to be against good players who just disappear (and reappear unexpectedly), screwing up ratings (often for periods of time substantial enough to affect players' matchups for a month).

Also if real life happens the good players will either quickly put themselves onto vacation mode if they have some time, if not then whatever happened was much more important than a rank on a ladder on a game, so I don't really see the problem.

Again, it's not worthwhile to just throw out assumptions about players if you're not going to bother actually validating them.