Hello, when i cosntruct my 40pts deck along with my teammate, can we both include two Lukes or two Hans? If so could i play Make my own Luck only on my own Han or also opponents? (TOTALLY UNTHEMATIC ALL THIS...)

Also, can me and my teammate include two copies of the same command card in our decks? (e.g TOUGH LUCK in my command decK and my teammate TOUGH LUCK also. Is this legit?

Each player builds his army individually. The restrictions applying to a single army apply to a single army, not to your opponent and not to your team-mate.

See the 4-player skirmish rules from the Return to Hoth, Jabba's Realm, or Heart of the Empire rulebooks.

I just want to add that keeping the unique restriction (only one Han, one Luke, etc.) is really fun in 4-player skirmish. It adds a pretty cool layer to squad building and thematic play. I've only played one such game and we played 2v2 of Empire vs. Rebels adhering to only one version of uniques allowed. It was a great match and seeing so many different minis on the board was very rewarding. I highly recommend at least trying it.

I think the rule is intended to make pick-up games easier so that two people can just whip out a pre-made list and not have to worry whether they have any duplicate conflicts with their prospective teammate. However I think if you are able to plan ahead with your teammates, enforcing the uniqueness rule across all the lists would be the way to go to make things more interesting.