Better take a hard look at War Engines which already allow this then.  I don't see how or why this would open up any doors to confuse assaults.  This is a very specific situation that has little relation to anything else.  In assaults you fall into one of two categories: ground or skimmer.  If you aren't one then you are the other.  We're not talking about an endless variety of combinations here.  At least, I'm not.

However, several people have alluded to combat initiative - where the attacker determines the kind of combat that will take place. So, how about this as a concept (the words will need tidying up) :-
When attacked, Skimmers may always choose to use their firefight value in an assault, even if there are enemy units in base contact with the skimmer. This represents the skimmer lifting off the ground out of reach of enemy ground units. When initiating the assault (even against other Skimmers), a Skimmer can declare the kind of combat that will take place (Close Combat or Fire Fight) which represents the advantage of surprise etc. In either case, the enemy must also use the relevant Close Combat or Fire Fighting values.

And what about my suggestion of allowing the initating Skimmer to choose whether to combat will be CC of FF??

A great idea, even better than Moscovians initial idea. I second that.

Rather than regurgitate it though, I'd recommend reading the original SG banter between Greg and I.  This thread will make a lot more sense then.

Guys, are the Eldar Shining Spears the only skimmer affected by this because they have better CC than FF??