The big difference is that Entocort is considered topical and prednisone is systemic. Sometimes there is so much inflammation going on, you need the systemic approach, especially if you have extraintestinal manifestations. For me, it is only for the arthritis flares that I use the prednisone, but my pouch usually is acting up at the same time (probably because of all those inflammatory molecules racing around in my body).
I would think that you would not want to use prednisone more than a few times a year, not a week a month. Even for joint injections, it is 2-3 times a year for any one joint, and it stays within the joint.
Entocort is a different story, and is considered a maintenance drug for steroid dependent folks, because it is topical. If you don't want the entire GI tract exposed, they do make it in enema form, which would be a more targeted approach.
Jan