I'm reading through the scourge of the grey quarter, and it brings up good points. The fact that the dunmer in riften have successfully assimilated with the natives there, the happily contribute and so are treated equally in the city. Where as they have an entire section of Windhelm to themselves, and yet refuse to contribute to the city. While the argonians are forced to live in a single room despite every argonians working for their pay at the docks... Seems very backwards to me!

You're not the only one feeling this way. Start reading the "Which side is more beneficial to Morrowind" thread and you will eventually see an argument discussing this.

One of the dunmer farmers who sells his wares in the city told me this: "Only trough hard work can we win the trust of the Nords"

Other in-game books say that Riften had a very hard time assimilating a large population of refugees.

Windhelm was probably following a "live and let live" principle set forth in the http://www.uesp.net/wiki/Skyrim:Decree_of_Monument. My guess is that it was as much the Dunmers' idea as the Nords' that they would be given their own district of the city that they would self-govern, as the Decree states. Only the Dunmer being Dunmer, no one could decide who should be in charge and none of them were going to knuckle under and do menial work for the Nords (as is still the attitude of some). So it doesn't take long for a community to go south under those conditions.

My guess is that the Argonians are kept outside the city to prevent conflict with the Dunmer, since the Argonians invaded Morrowind after Vvardenfell in revenge for centuries of enslavement.

let me guess someone stole your sweetroll

Look at the themes of the two cities. Windhelm is ruled by Nords that hold strength and honor above all. Rift is a wretched hive of scum and villainy.

You weren't supposed to take that book at face value. Critical reading skills, please.