WARNING: This video contains rapidly shaking/flickering images which may cause motion sickness or epileptic seizures.
Let's become the Titan of Ether and blow this poor controlling, stunlock-ridden, overly frustrating and incomplete popsicle stand once and for all!
So, what's our lesson this time?
...Well, alright, that's not true. For all its problems, Pagan does show a modicum of realism by having a pretty interesting moral dilemma.
The good of the Avatar's actions on Pagan are dubious at best; he carries out a murders to advance through the Sorcerers' ranks and eventually seizes power from the Titans themselves, resulting in devastating natural disasters and an enormous power vacuum left after their destruction... all so he can return to Britannia and stop the Guardian. However, it is established quite clearly that the four Titans are in the service of the Guardian and that they clearly do not have the populace's best interests in mind, so one could argue that they come out ahead in the end despite the suffering the Avatar brings upon them through his actions.
More than anything, Pagan perhaps best highlights the moral and tonal shift that the third arc of the Ultima series introduced, showing that heroes rarely achieve a total victory and that doing the right thing doesn't mean being popular with everyone (or even the majority of people). Ultimas 5 and 6 were pretty one-sided in their morality, but 7 and Pagan show that there is always a gray area, and that sacrifices often have to be made for the greater good. Which is a lesson a lot of modern RPGs could take notes from, incidentally.
Something else to note is that Ultima IX's original story (the "Bob White Plot") heavily implies that the Avatar is unwittingly acting in accordance with another of the Guardian's plans. Namely, that the Guardian is discreetly manipulating events throughout Pagan and Ascension, forcing the Avatar to commit reprehensible acts in his quest in order to sow distrust between him and Lord British, which would eventually set the two against one another and leave the Guardian free to destroy Britannia unimpeded. However, this is completely discarded in the released version of Ascension, with the story almost entirely rewritten and most of the FMVs created for the original plot repurposed (which results in nonsensical elements like the Avatar summoning Pyros in order to open a dungeon).