I'm under the assumption that Morroblivion is meant to be debugged (mostly) and includes all NPCs, quests etc from Morrowind.
Within my first 10 minutes I noticed several issues.
- Right after you collect your papers and you go through the building (before you exit to the barrel that contains the engraved ring of healing) there is not meant to be a NPC standing there. Normally you'd steal everything from this room and sell it as soon as you exited the census office but this NPC makes it impossible to take anything. Regardless of whether or not this was intentional or not, it most definitely isn't native to Morrowind.
- Hrisskar is missing, this also makes a specific side quest impossible.
- Side quests like Death of The Taxman and such are not prompt by the typical prompts (rumours and Socucius Ergalla).
- Guards do not attack a civilian who has drawn his blade on you first.
Has this already been addressed somewhere? I feel it's a right shame to be missing NPCs (especially when they prompt side quests) and even the side quests themselves (even present NPCs that should prompt them, don't). Perhaps I was over expectant when I read somewhere that 100% of the content would be available in Morroblivion and such.

Most of these NPC's you can't
Most of these NPC's you can't find are likely to be wandering off somewhere, since they were given custom packages. Hrisskarr is definitely in the game, for instance. He only spends quite a lot of time wandering around the far-off portions of the town, desperately searching for the gold he needs. He comes to Arille's Tradehouse only in the morning. This can be mildly annoying in multi-story buildings like the Legion Forts or Ebonheart, where you can spend 3-4 minutes wandering the building searching for the NPC.
I've completed quite a lot of very minor quests in Morroblivion (like Rabinda's Inner Beauty, for instance). From the uespwiki page on Death of a Taxman, I have the impression that the quest actually starts when you find his body, not when you hear the rumours, that are just a signal for you to investigate more.
The guard system is basic Oblivion one.