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The most common misconception people have about West Mexico is that it wasn't ever part of Mesoamerica until maybe the Late Postclassic and even then, they weren't quite Mesoamerican enough. This misconception largely has to do with a combination of factors.
The first is probably a lack of any sort of Florentine Codex-esque document. Michoacan has the Relacion de Michoacan which is a three part tome that covers the Late Postclassic Tarascans, but unfortunately two of those three parts are missing. The modern areas of Colima, Jalisco, and Nayarit never really had a Relacion type document. And in Jalisco they had a conflict in the 1540s called the Mixton War which resulted in many deaths and many people fleeing to more remote areas like Nayarit and Zacatecas. So even if a priest had wanted to make a Florentine type document, he may not have been able to.
Second would probably be the lack of steady academic and research interest in the region. Work has been done here and there, all of it very important to our understanding of the region, but it hasn't been consistent. There was an expedition by Ales Hrdlicka and Carl Lumholtz around the turn of the century, some work here and there during the 40s, a flurry of work in the 60s from UCLA and other Californian institutions, and then some putzing around in the 70s and 80s with some increasing work being done in the 90s, early 00s, and now. And because it hasn't been consistent
(Third) what information we do have about the region is strewn about here and there with chapters in books, old articles, and hard to access resources. There's no real comprehensive text that combines all of it into a general history for people to work from (i.e. Michael Smith's The Aztecs or Stephen Houston's and Takeshi Inomata's The Classic Maya) which makes it hard for people to learn about the area and become interested. Some Wikipedia articles are in sore need of updating with new information, new interpretations, new everything.
Fourth, West Mexico lacks the tall pyramids found elsewhere in Mesoamerica. Don't get me wrong, the yacatas at Tzintzuntzan, Michoacan are impressive as is Los Guachimontones in Teuchitlan, Jalisco. But they are no Pyramid of the Sun at Teotihuacan or tall stepped pyramids from Tikal. Unfortunately, early archaeologists like big buildings. And some archaeologists (like me) still like buildings, but understand that size isn't all that important (wink wink). What matters is what you can learn from the excavated buildings. Be it a few post holes in the ground marking a perishable structure to giant pyramids and palaces. Luckily for me I have been involved with current researchers who are willing to do more work and willing to publish in widely circulated journals and willing to get that information out there so that we can all benefit from having a more complete understanding of what was going on in Mexico in the past.