Considering how Imperials treat prisoners, they can hardly shout war crimes.
They're prisoners, i.e. they're there for actual crimes committed, and Valen Dreth is quite possibly the worst example to use as he's an asshat of the highest order. One can infer from his character that he actually committed crimes that merited his imprisonment for eleven years. Comparing his treatement by the jailer or that of enemies of the state during a time of war to the summary execution of innocent non-combatants including children and the elderly is like comparing apples and cow-patties.
By supporting the Empire does that mean you agree to a bureaucracy in which the ruling body of the Empire are the extremely wealthy that buy their Elder Council seats?
The Elder Council seats were only "bought' during the reign of Pelagius II because of his need to payoff the tremendous debts his father had incurred for the Empire during his reign. While the Elder Council has always been constituted by the wealthy that's merely a reflection of the fact that wealth and power go hand in hand, not that the seats literally go to the highest bidder. Seats are obtained by political intrigue and machinations by the most powerful families in the Empire who happen to be (surprise!) wealthy. Just what exactly are you comparing this too in an unfavorable manner? The fuedal monarchy of Skyrim where each Jarl is Jarl by virtue of lineal descent? At least the Elder Council has some sense of meritocracy in who gets a seat. In Skyrim you get to sit on a throne because you're daddy is the Bear or Istlod.
Taking into account the Eastern Provinces when they were part of the Empire, much could be said for the Northern.
Eastern Provinces presents one point of view about the benefits of having Morrowind and Argonia as part of the Empire. While it has some valid points, it's a decidedly lopsided view of the situation. The presence of the Imperial Legion in Morrowind isn't for the protection of Morrowind from outside forces. It's presence esablished a concession of a considerable part of the Tribunal's and Morriwind's autonomy under the Armistice. Likewise the protection of the slave trade by the Empire is a concession for Morrowind's voluntary yielding of said portion of autonomy and allegiance to the Empire. The book completely overlooks one of the most important things gained by the terms of the Armistice which is the surrender of Numidium to Tiber Septim which allowed him to finally conquer Summerset Isle and unite all of Tamriel underr the Third Empire. It also fails to recognize the real purpose in securing portions of Argonia (which is all the Empire ever actually controlled) to deprive pirates and raiders of their previous use of the coastal settlements as a reprieve from pursuit by the Imperial Navy and Legions. All in all it's a fairly shallow and narrow minded view as to why the Empire devotes resources to the Eastern Provinces.
Back into Skyrim.
"Damn you Stormcloaks. Skyrim was fine until you came along. Empire was nice and lazy."
This is simply a reference to the fact that Empire had no need to infiltrate the countrysides of Skyrim before the Stormcloak rebellion and but for the Stormcloaks, Lokir would never have been caught up in their trap for Ulfric. Regardless of how he characterizes it, it's literally no proof at all of the Imperial Legion's laziness in carrying out it's duties in Skyrim when examined contextually. It's in fact quite the opposite. When the Imperial Legion actually needs to do something, it does it quite proficiently as Tullius successfully trapped Ulfric.