Even the supply line idea is present in MoO, but by the time it would be needed to balance the game, it doesn't matter anymore.
In MoO, ships have a limited range, based on their fuel cell technology. If a ship is stranded too far away, it will automatically return to the closest colony (which doesn't make any sense, considering that it was limited by the fuel cells, but whatever). So if you the closest colony to your currently targetted system, your attack will be cancelled. Too bad, after a while you can research better and better fuel cells, resulting in Thorium Fuel Cells which provide infinite range. So while this again limits the expansion in the early game, it is useless in the end game.
I really wonder if all these things were added in that fashion to make for more challenging middle games and quick end games or if it was actually just a balancing error.
Maybe they decided it was not desirable to have a more balanced end game because the game would get too slow paced then. That's a really interesting question for me, as I never thought about similar game design issues yet...