Fyron,
Many of your concerns are in fact addressed as you become more familiar with the game. But I will be the first to admit that there is quite a learning curve. If the documents were good, they would have all the nations with units listed with their flags in color, right? Well...the documents aren't that good...but the in-game help is at least acceptable.
I will have to concede some of your points on the interface. But information like what troops are in an enemy territory will probably be put into the basic province info in the patch as multiple players have mentioned this. Well...one can hope.
Tax income is simple...just add all the incomes of all the provinces you control plus all the gold-generating structures you possess. Why does it vary from turn to turn? Dominion, positive or negative. From your favorable dominions of order, growth, and productivity you will get additional income. Lucky events can also add to your income for a particular year or subtract from it if you are unlucky.
Resources also vary with dominion. There are moreover some really, really bad events that cost you population on a permanent basis.
What information would you like to see in log Messages? Just curious. A number of additions which would not be all that difficult (I wouldn't think) have been proposed by various players.
To correlate nations with flags...this is easy...just go to "score graphs." Hover your mouse over the flag you are interested in in the graph legend. And you will see what flag corresponds to which nation.
The AI will often amass cheap units that aren't all that great in large number. Especially Ermor. The other AIs don't know how to deal with Ermor, so I would just exclude that nation from SP games. If you are building resource-intensive troops and your enemy is building non-resource intensive troops it will be easy for them to amass more of an army than you can. Also, if they have many more territories than you do...well...they will have more income and more centers of troop production. I disagree...I don't detect any hidden cheating bonus. Keep in mind that troops may be summoned as well as bought.
There is a very simple indicator of whether you have troops in a territory. Look at the territory (assuming you own it). If you have troops there, you will see a blue rectangle of one size or another. The size corresponds roughly to the number of your troops.
You are the first person I have ever heard call dominions unsophistocated. I beg to differ with this assessment.