The Beyonder was a controversial character amongst creators. Creators felt that Jim Shooter had abused his role as editor-in-chief, and forced the use of the omnipotent character upon other writers and editors. Some critics felt the crossovers didn't always mesh well with the main book. One of the most vocal critics was John Byrne.
Apparently, Steve Englehart wanted to tie in the Beyonder to older characters known as the Beyonders (first mentioned in the team-up comic Marvel Two-in-One #63, beings powerful enough to collect planets) for his "Secret Wars III' story in Fantastic Four #318-319. According to Englehart, editor Ralph Macchio hated the character and ordered the Beyonder "removed" from the Marvel Universe. Englehart did as asked but has stated that he tried to exile the character with dignity. The character was subjected to a retcon making him less potent than originally determined, and explanations of his omnipotence have been written off as the more powerful beings "playing along" to ease the Beyonder's transition into self-awareness.
Originally posted by golem370
Like I said that was a plot device. And there was no real knowledge of how powerful LT was then..