I think the first 4 points are easy for most of us to agree on. Point 5 is where things get contentious. Some of us view the Aztecs and Inca as stagnant, tribal states that simply couldn't accomplish much. Then there are those of us who view them as relatively normal states, just with a unique geographic and technological position. The former group tends to favor leaving these areas alone, usually citing that the game is about Europe and that these states are just fodder for colonization. The latter group generally wants to see a better representation of the history and uniqueness of these states because it expands the scope of the game. I personally fall into the latter group. EU4 seems to have fixed much of what EU3 got wrong. Native states are no longer completely helpless even before the Europeans arrive. Still, PDS failed to provide any accuracy in the setup or mechanics for these areas, which is disappointing. Mesoamerica doesn't even vaguely resemble real life and the Inca Empire is far too big at the game's start. These are the kinds of things that need to be fixed if the game is to be grounded in history.
Honestly I haven't seen anyone arguing that the Aztecs et al were stagnant, tribal morons who did poorly due to insufficient forebrains. Many have argued they wouldn't be anywhere near Europe in the EU timeframe if left alone, and I'm not sure if anyone disagrees. Few have argued that playing the native Americans shouldn't be fun, certainly not Jomini who is the one person I have seen put forward a reasonable and plausible suggestion for how to better model the Mesoameriancs in a way that is reasonably historical and still enjoyable for the player.
The rest of it seems to have degenerated into mostly irrevelent and poorly defined tangents like how likely Aztec weaponry is to break on metal armor and exactly how long it would take Spain to take over if Cortez failed. The former is frankly irrevelent to the game, this is about grand strategy not dueling tactics. On the second everyone seems to agree the Europeans should take over sometime in the 16thc, so the details are not terribly relevent either.
Unfortunately, at this point it is unlikely anything will change, I imagine they are down on the priority list and there is such a thing as an opportunity cost. Maybe in a mod or DLC though.