Gah! This is why games aren't more moddable. People confuse mods with features, and blame the game designers when it doesn't work out. CA could have made the max men limit hardcoded in a binary file, and then you would never have had the chance to whine about have to change a single line in a text file in order to mod the game.
Some limits are required in order to make sure the game can be tested on a range of systems. For those who wish to take the risk of pushing the game into untested territory, the devs made modding this easy. But if it is in game it has to be tested. Just be thankful that modding this is so simple.
As for your other points not saving preferences for settlement management and graphics etc that would clearly be a bug, rather than bad design, although if it is a bug I have never heard reported before (same for everyone else in this thread) so it seems strange. I've certainly never has such trouble with MTW2.
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