Do you think there will be a Flash/Supergirl crossover episode this season?

I don't think so. Even if they didn't go all out for Crisis on Earth-X, the scheduling shake-up for Supergirl episodes makes it so their production schedule doesn't line up, anymore.

To be honest I kind of want a Supergirl/Legends crossover. I want to see Sara catch up with Alex, (not hooking up again, but giving her some more advice).

Also I want to see Mick loose in national city, just to see the face of the DEO when they are informed they can do nothing because he's technically a good guy.

Highly doubtful, they put all the available crossover time into Crisis on Earth-X.

On top of the other valid points made here, it's also unlikely because we haven't heard about it yet. Remember all the hype and coverage of the first one and the musical?

I would really want to see Supergirl cross over with more than the Flash. When the Wave Rider crashed in LA (where the CW recorded shots of "National City" I was so excited because I thought that they had accidentally arrived on Earth-38. Also, the relationship between Oliver and Kara shows a lot of promise in the crossovers, so it would be nice to see that develop.

I don't see anymore crossovers this season after the Crisis On Earth-X until the next annual crossover.