So, this relates to casual Skirmish and not competitive for obvious reasons. But, when I've played Skirmish with friends, I supply the game, we choose different factions and then choose our command cards. So deployment cards are not an issue but command cards are. The issue is that both players might want the same cards. I'm wondering if and how other folks deal with this. My most recent way to handle this:

1) We sort the command cards into 3 decks based on cost values (1 pt, 2 pts and 3 pts). Then each of these decks are split in two and each player gets a set (half of each deck). Of course, if their are character specific cards then we hand them to the owner of that faction.

2) Each player then looks through the their command card options and chooses what they want.

3) We then trade the decks of unselected cards so that you get to choose the leftovers from your opponents decks. The downside is that, if you were really savvy, you could probably deduce what your opponent had selected, but this hasn't been a problem (yet).

Any other strategies?

Draft any cards that both players want. Aside from the doubles from the core set that you'll already want I'd just grab the solid cards that you both want and then go back and forth with them. There honestly shouldn't be too many overlaps. Just things like negate, positioning advantage, etc

On second thought I'd probably just straight ban Take Initiative and Negation if you don't have two of each.

You can always proxy cards though. Just throw a slip of paper with the name of the card into the sleeve with a different card and you are all set.