Entocort has the advantage of being topical in the gut and poorly absorbed into the blood and quickly metabolized once it's there. This makes it less likely to induce side effects than the more systemic prednisone. Entocort is also "timed" via pH to release in the ileum region of the gut allowing it to be more specifically focused on the area where your disease is located.
It's true that Entocort is generally "weaker" than prednisone, but given it's advantages of being more narrowly focused on the ileum and with a better side effect profile, my guess is your doc thinks it's worth a shot and wants to try it.