yes the multiple players with the same colors has been brought up to pasik before. Not sure when he will decide to deal with it but I am assuming that the jeep mechanics are more important right now.
There is 12(!) different colors by now, but obviously that's not enough in the long run. It's difficult to find very distinct colors without making them all shiny and annoying. Feels like I'm back to EGA times, 4 more colors to spend, and one of them is given to squad AI already. There also seems to be a bug that the map marker colors do not stay that well in sync with the field/edge marker colors.
OzyThesage's suggestion about the shape might be the way out here. Initially I was thinking that it would make them appear distracting and inconsistent, but maybe it doesn't matter that much in the end.
And yes, jeep is #1 currently.