I think scenarios are an entirely different ball of wax.
Don't fit into the usual mold, for this argument. IMO there are so many reasons to pick axis or allied (and often reasons for either at the same time!) that it's a personal decision each and every person must make.
I wanted to fly Rangoon for the P-40 (I got a -B model, but I still flew it!) and the history aspect of it.
I wanted to fly allied in Downfall because of pals/squaddies flying allied, and I wanted to wing with them, teamwork, coordination, the whole shebang.
I wanted to fly both sides of Tunisia. I like 109Fs in N. Africa, the whole Marseille mystique, and I like 190s, but on the other hand I have a soft spot for the P-40Es and P-39Ds as well! As well as I'm a B-25 fan and that was really one of the strongest draws for me to join the allies. In the end several folks in my MA squad were scattered on both sides of the event, and I ended up choosing C202 as my primary (having a love/hate relationship with the ride).
So it's always case by case for scenarios, always subjective, and I would count that separate from FSOs/snapshots/etc where folks get in a rut. To me the scenario is a bit more "special" than 'just another setup this week, might as well make a fast choice'...