While it's certainly true that EU favours Europe, I don't think that's the main issue here. I did an analysis and Anatolia is not particularly too poor compared to, say, France. (It's not perfect, but compared to the problems with India, China, Viet Nam, etc. etc., and allowing for the fact that ratios of population between countries could change significantly over 4 centuries but they don't in game, it's a decent approximation.)
There are four areas in Europe that are substantially overpowered even compared to the rest of Europe: Sweden, Austria, Super-Aquileia

(I have no idea why Cortes went all the way to Mexico when Aquileia had just as much gold as the Aztecs), and Greece. Historically, the population of Anatolia outnumbered that of Greece by a factor of something on the order of 4:1 or 6:1 during this period. In EU3, before 1453 the Greek provinces have the same tax base as the Turkish ones. Even after Constantinople gets reclassified as Turkish the Turks only have a 4:3 margin. Again, this is because the Greeks are far too numerous, not because the Turks are especially badly represented. So yes,
of course if the resources of the Greek peninsula had been 5x what they historically were, Byzantium would have stood a much better chance of surviving the early 1400's. And of course the Turks would have had more issues controlling Greece if there had been as many Greeks as Turks.
Well put and I mostly agree. I still think the comparative generosity towards the west is playing in here however as we're seeing a lot of Castillian and English naval invasions completely destroy the turks. I made a spreadsheet back when I started modding eu3 to check the manpower average of certain regions and compare that to approximations of historical populations (the latter I got from Angus Madissons data). I'll leave a few examples of these observations at the bottom of this post.
It is indeed obvious that Greece is overpowered compared to Turkey. I'd also agree that the situation isn't nearly as bad as in the far east or even Northern Africa. Still, other countries that perform well are given big boosts in general in EU3. Sweden for instance has a manpower far above what it deserves, probably due to the fact that it would otherwise never perform close to historical given how dependent EU3 is on manpower and taxbase.
Turkey on the other hand has not. The Ottomans supposedly just trounced a crusade of many of Europe's finest armies at Nicopolis. In the game however their starting resources hardly lets them compete with their historical enemies. Most of the time they'll be a victim of a crusade within the first 20 years or so from which they will emerge trounced, if alive at all.
Here's a few examples from the spreadsheet I made. As I collected this data with IN it's outdated now but I'd say the same tendencies remain. Also there's bound to be some errors due to rounding or the possibility of me using a definition of "France" that's different than that of the people who calculated the historical population.
One could also question if manpower should be tied to population. Population is after all not the same as potential soldiers. One could also argue that averages aren't that important when comparing countries as I presume to do (I do think they are though as that's the only way I've found to account for both the uneven distribution of provinces and the actual manpower values of the provinces).
Greece has a manpower average of 2,67 per province for a historical population of, on average 0,11 millions per game province.
Turkey has a manpower average of 2,94 per province for a historical population of, on average, 0,39 millions per game province.
Morroco has a manpower average of 1,45 for a population average of 0,14 per game province.
Portugal has a manpower average of 3,33 for a historical population average of 0,17 millions per game province.
The British isles has a manpower average of 2,35 per province for a historical population average of 0,17 per game province.
France has a manpower average of 4,73 per province for a historical population average of around 0,37 per game province.
Sweden has a manpower average of 2,35 for a historical population of 0,04 million per game province.