Depends on what your goals are. If you are aiming to use the FF miles for a big trip, you are better off having one program so you can book onto the same flights (e.g., call UA and say we want these 2 tickets funded from these 2 accounts) and not worry about fleeting inventory or not having enough miles for 2 of the tickets.

On the other hand, if you are mostly flying on cash tickets, having status in two different programs can give you more flexibility on those cash tickets since you may have both E+ and MCE access and free bags so you can truly just buy based on price since you'll get E+/MCE for free regardless.