Custom games should be split in to ranked and unranked. This can be differentiated in however way makes sense, such as leaving "custom game" option as is and adding a "ladder game" option. However, functionally they are identical other than two things: the fact one tracks stats for ladder participation while the other does not, and that the ladder mode is only official gameplay (no game modifications (not necessarily inclusinve of UI mods, if such thing ever happens)) and game settings.
This divide accomplishes a couple needs: the need for players to be able to play with friends; the need for players to play the game they want (even with some limitations, such as game mods and settings) such as map, number of players, quality of players; the need for players to have a sandbox ground, where they don't have to feel pressure of doing good or bad.
Ladders can have specific modes, as well - 5vs5, 3vs3, etc. Pantheon and skirmish, then, fall in to the ladder system as would be expected.
However, pantheon and skirmish are different in that the deal with auto-matchmaking. Now, it must not be forgotten the point of auto-matchmaking which is to, in the ideal, provide competition that is equally challenging for all. The matchmaking aspect of pantheon and skirmish games has to take in to account individual player ability in a way that is robust and reasonably accurate. The topic of what stat tracking is needed to facilitate a reasonable skill estimate is for another topic, but that goal is paramount.
A person's individual ranking will be used in match-making; a person's individual ranking will be determined by their rankings in the broader ladder system.
If we make the assumption that level of stat tracking is in place, then things start falling in place.
The ladder system grows accurately, allowing all manner of ladders without this annoying bickering and extremist pushing of some people.
Pantheon and skirmish can be expanded to have relevance on the game (ie, actual rewards for participating in pantheon or winning the epoch so that, you know, maybe people would actually play the pantheon which should be a major draw).
And this while still offering an arena for people to simply have fun with their literal custom games, as well as to just goof around.
This is robust. Everybody wins.
The only starting point should be stats. No amount of fiddling with the current ladder system matters if the rankings don't make any sense. Leave everything as it is now and focus entirely on that. Once the stats are done in such a way that people are reasonably ranked on an individual basis, then and only then can ladders be built.
I am seriously tired of people trying to solve the problem without actually addressing the problem. The problem isn't custom games. The problem isn't premades. The problem isn't skill. The problem is inaccurate, non-personal rankings that the system is built on. This is a very hard thing to get right; I am not knocking whoever has been working on it. But it is the root issue. Address it and ONLY it right now.
For the people turning it in to a premade-debate. Shut up. You don't have any clue what you're talking about; it is completely irrelevant to EVERYTHING needed for a robust and accurate ladder system, and is certainly irrelevant to frogboy's question(s).