Hmmm... long batch of replies this time! I'll do my best to address everything that was said!
Italy - I completely understand some of the sentiments that northern Italy especially shouldn't be a rollover for the Komnenids, and if you look at the story, it wasn't. Southern Italy was the origin and final stand of Basilieia's rebellion against Manuel, and two federations of northern Italian city states backed Leo Komnenos' rebellion in southern Italy in the early 1200s after Thomas I's campaigning in the north. Thomas II then reconquered the area, only to have it revolt again during the chaos of 1216-1220. The only reason it hasn't revolted since is likely because Bardas Komnenos' invasion was so devastating--the old city of Milan was completely torn down, brick by brick, and the survivors, barely 10,000, had to rebuild their city a few miles away. Off the top of my head, Florence, Pavia, Pisa and Bologna were at least sacked.
As for the larger ports of Genoa and Venice, initially they were a part of the revolt, but regardless of who owns them, they are still prime commercial locations for goods from the East to enter Europe. They still have some autonomy (there is likely a Doge still, for example, and both are part of the imperial desmense, they report directly to the Emperor, not some Prince), and they're plugged into the largest and most secure trade network in Europe. That's cowed the independence hotheads, but only so long as that trade network remains secure. If war galleys start crisscrossing the Med instead of taking down pirates, both city's could quickly change their minds.
EU3 Portion of This - Still a long way from it, but I've decided I'm going to handle the last infamous reign as a dual project--it will be a historical denoument here in CK, and posted simultaneously in the EU3 thread (yes, Rome AsundAAR), as the introduction..
Nikephorian Army Setup - Call it what you want, it's an attempt to reign in wider parts of the empire through that most Byzantine of things, making new offices and titles. The basic idea for this could trace back to the old OTL Late Roman legionary system, based around frontier defense forces to conduct everyday work and slow an invader, field armies to repel serious challenges, and finally an imperial reserve to act as an ultimate backup. However, as people have pointed out, it leads to all sorts of interesting what ifs... if the CinC of the East decides he should be emperor and revolts, the system has automatically broken down, regardless of whether his subordinate army commanders respond to his call or rally around the flag. For better or worse, this is the army organization that'll see the Komnenid Empire through some more glorious triumphs before its ultimate collapse and ruin.
Komnenids and Ethnic Relations - The Komnenids bear alot more resemblance to the Middle/Early Byzantine Empire than OTL Komnenid Empire with regards to other ethnicities--the Byzantines are big, so they feel alot safer about coopting native elites, and turning them "Roman" (speaking Greek, Orthodox faith, loyalty to the Empire). You likely wouldn't see a Massacre of the Latins at this point in the empire, though once the empire gets wobbly, questions of "well who is Roman really?" will start to take more poignancy. Of course, like in OTL after the collapse of the old Roman Empire, you'll have all sorts of people claiming they are "Roman" and their neighbor is merely a "barbarian...
On Andronikos - :rofl: All you know right now is there's something wrong with his eyes, and he likes to play musical instruments. That doesn't necessarily make him a sociopath, or Nero, or a great culture artiste, or Manuel reborn. It makes him an 8 year old kid who likes to play the lyra and has a problem with his eye.
On Hunting Accidents - Red herring, or significant plot point? We'll see next update!
On This Story Making an Impact in Sales, etc. etc. - No idea, but very high praise... thank you.
I spent most of the weekend out of town so I haven't had a chance to write the next update.. however, I do have outlines for it and the following six or seven done. I'd say the update should be up probably Wednesday, perhaps Thursday. So I'll leave you with the piccies I've chosen for three new major characters in the story that will be shortly introduced (next update).