The counter argument to that is not that the native Americans should "lose by default" - but that by giving them more advanced tech than they had historically, you'd be making them less realistic and less fun to play.
At the moment, playing a native American nation in EU3 is a big challenge - but it's possible to win through with skilled play, and you feel a sense of achievement when you make it. What some people are arguing for is to make them basically European nations except with more obsidian and feathers, that have almost the same capabilities - and so playing them would be pretty much the same as playing a European power. In which case why bother?
Frankly that's Illapa. Most of have been arguing that Natives should essentially be like a very backward Old World nation in terms of gameplay. Currently there are a few specific rules unrelated to history that are used to nerf the New World. So no, the bad but not unusable units and 30% research rate I mentioned earlier are not the same thing as making "them basically European nations except with more obsidian and feathers". The ability to survive as the Natives, once more, is not a declaration that their gameplay is sound.