No it isn't. You can argue about whether or not that was the primary reason for their defeat (probably not) and how well they are represented in EU3 (not very) but in many (though not all) ways the native americans were technologically inferior to europeans. (not neccessarily through any fault of their own, mind)
I agree. Putting them on the same level as Europeans is ridiculous. The level of nerfing they receive in vanilla is equally ridiculous, but there's no reason to try to overly buff their technology either. I usually advocate a 30% or so rating and a starting tech of 1 (compared to vanilla's 10% and 0 respectively).
Put it better than I could myself.
Sure comparisons are hard and you aren't every going to get a complete match, but when you break their advancement down to 5 tech levels ancient Egypt would be a good comparison.
Once again, it mostly depends on what you're talking about.
Government:
Despite being quite brutal, the Aztecs were not actually a tribal people. The Aztecs were essentially an elected, theocratic monarchy with a set legal system and a structured government. The Inca were also not tribal by this point. Their government was an absolute monarchy. They had very well established systems for law and taxation. These qualities are not particularly Egyptian and the fairly vague nature of government tech in and of itself also limits comparisons as these type of qualities could be said of many states.
Land:
It's very hard to make a comparison here. New World warfare was quite simply different. No cavalry. No metal. No one in the Old World, Egypt or not, was going to be quite like them in that aspect. And that has only a bit to do with technology and more to do with plain differences in warfare. EU's land tech system and units are not quite made to represent such a quality.
Naval:
This varies a bit. As we discussed earlier, the Inca had a naval tradition. They had ships and engaged in travel on open sea and occasionally launched attacks from the sea. The Aztecs on the other hand did not. Part of this has to do with them having little direct contact with the sea, but part of it also has to do with the lack of a true naval tradition. It's hard to represent that split between those two regions if we're to keep them in the same tech group. Nonetheless, Ancient Egypt was still developing ships and never gained much ability to go beyond their own coasts. Travel over open water was not really possible for them and thus South American nations had a clear technological lead there that makes them more similar to contemporary nations in the Old World than to the Ancient Egyptians. The Aztecs don't really resemble either.
Trade:
Trade is another elusive tech. Both the Inca and the Aztecs engaged in widespread trade and exchange. The Aztec Empire was essentially founded in order to siphon wealth and trade towards Tenochtitlan. Neither had a set currency, often using semi-bartering systems based off rare goods like cacao beans or luxury fabrics. This is a quality in common with Ancient Egypt, but the shift to a standardized monetary economy varies greatly across the world, having nothing in particular to do with Egypt (it could instead be compared the Medieval European economy and its use of labor and numerous different forms of coins as a form of currency).
Production:
Both the Aztecs and the Incas managed to support large populations easily comparable to the Old World. The scale of building and infrastructure is also comparable to their contemporaries. Production tech also tends to involve things like medicine, astronomy, and agriculture. These are all also quite comparable to the contemporary Old World. Ancient Egypt would not really be appropriate as the Ancient Egyptians lacked things like effective medicine or aqueducts. It would have been next to impossible for them to build and maintain a city like Tenochtitlan with their technology.
So I guess my point is that it really varies. Only land, naval, and production technology real show any clear cut progression over time. Land shows a clear inferiority, naval shows backwardness but not of ancient levels, and production shows relatively normal levels of advancement. Government and trade are a lot harder to pin down. Government varies greatly across the world and Natives weren't really any less capable of governing themselves than anyone else. Trade was not as developed as in Europe but some areas of the Old World would not have been drastically different overall. So Ancient Egypt really isn't a particularly good example, as they were ahead, behind, or similar in various places. As I stated before, we could easily draw comparisons to a number of different states.