Wow that's just... So ignorant. Native Americans did not think Europeans were magical or gods, and they adopted European technology extremely quickly, because duh, guns are useful. The biggest handicaps for natives wasn't technology, but their lack of numbers and organization. You can't exactly build an industrial economy with just a few thousand people- they were screwed demographically, and politically, not because they somehow were too stupid to adopt modern technology and adapt. Horses for example weren't introduced to the Lakota until the eighteenth century, yet they quickly became master horsemen, which together with firearms revolutionized their society, allowing them to hunt big game efficiently and dominate their neighbors. Yet their population in 1800 was about 8,000. If you want to nerf natives, nerf their manpower, not their tech, because once contact with Europeans is made, rapid advancement is inevitable.
I think its a shame you have decided to call me ignorant without understanding what I wrote, I will clarify what I meant. In the years directly post contact (and I that was the focus of my post, not the 18th-19th centuries) there were a number of native groups who it seems believed European's to hold magical powers or at the very least did not directly adopt it immediately (although these matters are rather difficult to discover when you are discussing societies that leave us relatively little in the way of written sources, sidenote in my game the Potawatomi have the printing press in the 1590's, this being a people with no agreed written system into the 1880's, but I digress). For evidence backing this look at early contact period artefacts such as those depicting early Dutch explorers in a similar fashion to local deities, or James Axtell's Through Another Glass Darkly (New York, 1988) which formed the basis of my earlier comments.
Regarding Muskets, the first record I've been able to find of their use by native's was by the Pawnee in the 1720's, this being of course 180~ years after their first contact in 1541 who had regular trade links with the French from the 17th century. I don't quite see how that doesn't reinforce my point that technological adoption by Native American's was slow and often patchy (certainly not chasing down Europe in the institutional or technological stakes). Furthermore, once again referencing Axtell (and others, I just happen to have access to that one at home) the native peoples frequently saw little to envy in the European way of doing things, for example see those taken to Paris in the 16th-18th centuries who expressed opposition to Feudalism, the obvious poverty of some within French society and that their dwellings were fixed and wasteful of space, I am willing to accept that they may be being used by European writers as convenient mouthpieces and so you can discount that if you please, however I maintain my point.
Coming onto population EUIV doesn't simulate the Virgin Soil Plagues (probably for good reason as that would be basically game over for natives), so it needs to do at least something to reflect that and I feel that perhaps making it hard to adopt institutions quickly from the European's would make sense, or at the very least allow you to choose as the colonial nation whether you want to share all your ideas.
I hope that has clarified my point, I would certainly agree with yours about the much later period, there was certainly direct adoption of guns and horses and they had a big effect. They also would have had little reason to see their contemporaries as anything other than men.