I can understand some of the disappointment that people may have with episode, given how "Smithers running the Power Plant" was a story that had a lot of potential that ends up getting wasted. My response to this:
1. It looks like the main focus of the episode wasn't Smithers running the plant, but rather rather Mr. Burns spending some time in jail, and in the end, that storyline had a lot of good jokes (i. e. Burns, as he narrates the flashback, inserting some "daydreams involving a sports car, some footwear, and a blue pill" just we get to the part where the flashback ends; the warden's helium addiction; the black prisoner mistaking Charles Manson for Jesus).
2. A lot of the blame for the wasted potential of the Smithers sub-plot can be put on the writers deciding to include a third sub-plot involving Bart and Lisa taking care of an ant farm. Outside of Homer mistaking the death of Lisa's ants as Patty and Selma's death and the background shot of Marge carrying cat food as Lisa talks about how the last surviving ant is on its last legs, the storyline felt more like something added to give Bart and Lisa some screen time in the episode. Also wasting episode time: the whole bit where "Flanderized" Marge is against Bart and Homer throwing rotten vegetables (and the bit where she makes Homer eat a rotted jack-o-lantern).
In the end, could this episode been better? Heck yeah, as we could have dropped the ant farm storyline and instead focus more on Smithers running the plant. However, I found the main focus of the episode (Burns in prison) to be decent.