... what? If you mean second to Planetarian. Of adapted media, the Little Busters source material is not second to anything.
(SPOILER)This is probably more a result of not having read the novel, so I'll explain, but you missed the point. The overall result is the same, everyone lives; however, the extra stuff in between is gone.
It was mismanaged in that JC Staff decided to gloss over the scene by playing stock music over it and having it take the all of twelve minutes. We've already heard the opening 20some times by now, yes, we get that when this music plays, it's supposed to be dramatic. When you're watching the show, they just walk on through the bus and start rescuing people like there's no issue.
In the original novel, there's two endings. The first time you reach the bus, you either die, or you run away. You don't have the option of rescuing anyone, because if you do, you pass out in the bus, and you die. This leads to a scene in the hospital, in which Riki and Rin both have to resolve to change the situation.
You have to come back to the bus later, after another scene in which Riki has to decide to be born and meet Rin. This is the actual result of the wish, to be reborn in a second timeline without any of the issues that would keep Riki and Rin from saving everyone. In the show, it's implied that the wish is simply to save everyone, which is the lazy way out.
When you get there the second time, there's a set of six choices or so that you have to get correct. Even after being reborn, Riki still has to make correct calls when he's going through and saving everyone. Just because he was reborn as a badass doesn't mean that he can't get everyone killed. A leader Riki may be, but a leader can still lead his people to horrible tragedy. JC Staff leaves all of this out, and makes it look easy, draining the situation of its potential full impact.
The original ending is only three hours long because of the text. From novel to show, you're missing out on quite a bit. You're missing out on Riki really stepping up to his new mantle of leadership, something that is gained through multiple lifetimes. You're missing out on the music that plays during the bus scene, the music of impending and immediate doom. You're missing out on how much smarter Riki and Rin got, in that they could stomp their emotions out, and rescue everyone in a timely order and without getting everyone killed. From what I remember, all they left in was that Kyousuke was stopping the gas leak. They never included how he was stopping it.