Well, for starters, what't the earning rate at the Choice portal versus the Marriott portal? In the same location, most of the time, Marriott hotels tend to require more in Marriott points per night than Choice hotels require in Choice points. Therefore if both portals earn you the same number of points, those points will go further with Choice than with Marriott.

OTOH, Marriott properties tend to be a bit more consistent. (But with both programs, I would recommend checking reviews of individual properties, because some Fairfield Inns aren't up to snuff just like some Quality Inns aren't up to snuff.)

If you travel to small towns (say, right outside National Parks), very often you'll only find Choice (and other budget programs), not Marriott (or any of the major programs). OTOH, in some big cities, Marriott may give you more of a selection.

So you may not want to focus entirely on one or the other, but use some of the above info to figure out a good balance for you.