Just looking at the kits I could MLS teams is that if they are blue they have a red away kit or if a red home a blue away. That seems to be in part because most of the color schemes in MLS are red & blue (fire, FC Dallas, prime examples). After, that generally works to provide enough diversity. Home Color schemes of shirts as of now by conference are:
Columbus: yellow (White away)
Dc United: Black (white)
New England: Navy Blue (white)
Sporting KC: Sky blue/Navy blue (Navy blue with sky blue)(3rd kit black with sweet navy/sky blue plaid)
Dynamo: orange (white)
Impact: blue (white)(black & white)
Red Bulls: White (navy)
Philadelphia Union: Navy/Gold (sky blue white)(black)
Toronto FC: red (black)
Chivas USA: red (navy)
RSL: red (white)
Colorado: burgundy (an unholy shade of blue)
Vancouver: white (dark navy blue)
FC Dallas: Red (blue hoops)
San Jose: blue (red)
Portland: green (red)(green w/ gold)
LA Galaxy: white (blue)(black)
Sounders: neon green (black)(another black, with even more neony green)
Now don't forget Orlando will be coming in with a purple shirt.
Based on the plethora of blue already there in MLS, I think the club may choose a navy blue only for a third kit and try to go in a different direction with the away kit. I like the idea of having an orange away kit, since only the dynamo use orange at all in their color scheme and when Houston plays NYCFC it'll obviously be orange v. sky blue. NYCFC could also follow most of the blue home pack and have a red one but I hope not.