They wanted Moriarty to return earlier and more frequently but they got tied up in litigation with the Conan Doyle estate for a few years...
First I thought you meant they wanted Moriarty to return after 'Ship in a Bottle' but did you mean they wanted Moriarty to come back sooner than season 6? That might have been interesting. However, I think 'Ship in a Bottle' is a nice episode, I wouldn't change history with the risk of losing that episode. On a TNG marathon that episode could be used as the series final episode, Barclay says "Computer, end program" and ending credits roll. I've done that once or twice. =)
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