While there was some foreshadowing such as Megan's description of a woman her father disappeared with, the prophecies of Megan's 'second coming' and most importantly, the prophecy made by the G1 Twilight, many fans considered it inadequate.
Broken Base: Over the last chapter. Some readers were thrilled. Most consider the story to be ruined forever.
Diabolus ex Machina: The now retconned chapter Eight's revelation that Celestia and Luna are really Tirek and Grogar, and that their benevolent reign was all to get the Rainbow Of Light from Megan eventually, spending a whopping 5000 years on this plan.