So. Ulfric is not a good leader because.
-He is racist towards certain races... argonians being the only proven race so far
-Windhelm is an old stone city that could use some repair? Not really sure. It looks great, just a little cold.
-He challenged the High King to a duel to the death as Nordic tradition allowed and the High King accepted and lost.
-Because Ulfric used his voice, the thu'um to show that the nord culture when any nord could learn the voice were letting this culture get lost in imperialism.
-Because Ulfric winning the war places him in a pretty decent position to take the throne as High King.
Now my reasons the Empire is not a good leader.
-Has lost two emperors to assassinations in the last 200 years. Strangely enough people seem to hate Ulfric more for killing the High King then the Dark Brotherhood for killing the last Emperor. 
-Has shown a complete and utter lack and disregard for its citizens and treats them no better then animals. (example your own unavoidable execution for simply being at the wrong place at the wrong time)
-Will without a second thought, allow countless lives to be lost for its own agenda.
-Has let the enemy occupy Skyrim and run unchecked and un controlled for over 20 years, kidnapping, torturing and killing citizens of Skyrim.
-Can't even show Ulfric the courtesy of sitting him down with the emperor and negotiating a truce.
-Tullius is so weak minded he can't even take accountability for his own actions and claims they knew it was the thalmor playing both sides all along. Well if you KNEW this why keep playing?
-For an being founded largely by nords, to then toss their own religion aside in the name of "peace" Peace for who? Not those in Skyrim. This would be like the US saying to ISIS/all terrorist groups who hate us. "Hey... you know if you stop attacking us we'll abolish Christianity. Oh, and while we're at it, You can as many military instillations as you want on our soil and we'll let you do what you want."
-Empires rise, empires fall. The empire is NOT the same one you loved during Oblivion so put down your nostalgia glasses and take a good look
-Tullius was so eager to kill Ulfric he didn't even bother trying to get him to Solitude for a fair trial. Did Ulfric deserve one? That's besides the point.
-Tullius was going to allow the beheading of a horse thief. Which is only a crime of a couple coins. 
-Tullius is such a child constantly looking for approval he even dared to bring Elenwen with him to High Hrothgar!
-Elisif who has NO royal blood. NO military experience. NO leadership qualities. NO backbone, hell she hires you to secretly take her husband's horn to a talos shrine. Shows me she can't even set a good example. She is the Jarl because her husband just so happened to be the High King. She is no more fit to rule then the president's wife taking over if he died.
-The empire is nothing more then a shadow of its former glory which even then was simply a nation setting out to concur the known world and bring it under its rule. Sounds like a bully to me.