I don't know why Bourbon is not seeing annexations in the GC. I saw plenty of them on Normal & I see plenty more on Aggressive. The AI does prefer to reparations rather than annex, but this is more historical than the alternative - most wars in the period were not fought to the extinction of one side or the other.
As to his particular examples:
Austria never annexes Bohemia,
I've seen this in most GCs, although the Hapsburg AI is often slow about it, & often allies with Bohemia instead. But then I've seen Austria annex Bohemia within the first 2 years of the game start also. It just depends.
Russia never annexes Kazan and Pskov,
Since 1.08, I can't recall a GC where the Russians didn't at least try to take out Kazan fairly early. Sometimes they succeed, & whack all the khanates within 20 years, sometimes it takes a century. The only time I can recall Russia not eventually getting to the Siberian corridor is my GC as Poland-Lithuania, where I allied with Sibir to close the door to Russian expansion, & eventually rolled him back to just being the Grand Duchy of Moscow.
and Turkey never annexes Mameluks,
I don't know - in my games they always try, often DoWing the Mams with their first diplomat. More often the Turks wait until they have at least 1 ally before they let the Mams know how they feel about Shiism, but annexing the Mamelukes never seems to be far from the mind of the Turkish AI.
England never annexes Iroquis,
This is one with which I agree. The game engine has some difficulties here. Part of it is that the AI usually keeps fairly small armies in the colonies, so taking out a 6 province nation is challenging. And the Iroquois cannot DoW anyone else, they can only respond to alliance calls or fight defensive wars. This means they are involved in fewer wars than most nations, and therefore present fewer opportunities to be annexed - which is probably wise, as they are a pushover.
Personally, I think the game has too many annexations, as opposed to too few. At the end of most GCs, the number of European minors has thinned out tremendously, while historically this was not the case. But the gameplay feels about right to me - which is probably the most important thing.