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Yes, territories were not really made to become states, in most cases. They were usually made when large chunks of unorganized federal land needed basic governance. Territories were created by Congressional decree alone. Territorial governance was set up and overseen by Congress.
Although states often took the name of a territory the process was quite different. States were created when the people in part of a territory organized themselves, drafted a constitution, set up the foundations of self-governance, defined boundaries, etc, and eventually petitioned Congress to recognize their statehood. Congress could say no, or, more often, make conditions, such as boundary adjustments.
All the changes made to Wisconsin, shown in the OP map, are of the “decree of Congress” type, not the “people of Wisconsin” type. Iowa would be a better example of an alternate state that might have been. As with Wisconsin, Iowa Territory was huge but it was obvious that only a part would become a state. Certainly nothing bigger than Missouri.
The Iowan Convention petitioned Congress with boundaries rather different from today’s Iowa. The southern border would be with the state of Missouri, and the east along the Mississippi, as today, but to the north Iowa would reach up the Mississippi to the Minnesota River (St. Paul), then southwest along the Minnesota River to the Blue Earth River, then diagonally southwest to the junction of the Big Sioux and Missouri Rivers (Sioux City). [This map](http://iowahighwayends.net/maps/proposedborder1.gif) shows the proposed northern boundary—this Iowa would have a large triangle of the rich prairies of what is now southern Minnesota, but not a smaller bit of what is now northwest Iowa. Unfortunately I can’t find a map of the full proposed state—it looks something like a pentagon.
To Iowans these boundaries were sensible and good—access to the Mississippi, Missouri, and Minnesota Rivers was highly desirable, as was the fertile soil of today’s southern Minnesota. Rivers were key for transporting agricultural goods. The Minnesota-Mississippi confluence, where Minneapolis and St. Paul are today, was of strategic value (transportation, trade, etc). It all made sense. This Iowa would be larger than Arkansas but smaller than Missouri.
But there was trouble in Congress—not over the sensibility of these boundaries, but over larger, slavery-related issues. Northern congressmen, in part alarmed at the adding of Texas to the US, wanted to make smaller states so they could make more free states. So Congress amended the bill’s boundaries, [making a much smaller state](http://www.mnopedia.org/sites/default/files/styles/multimedia/public/Map_5.jpg), without access to the Missouri River and not reaching to today’s St. Paul. Congress passed the bill, approving statehood, but it was rejected by Iowa voters.
Apparently this was the first time a Congressional offer of statehood was rejected. Anyway, it was clear that the main problem was the loss of Missouri River access, so the next year Congress made another offer, in the form Iowa has today, which was accepted.
As a postscript: Ten years later Iowa tried to do what Missouri had done before—add a chunk of land by extending their northern border west to the Missouri River. Missouri had done this (the “Platte Purchase”, in addition to the “Bootheel”). Iowa proposed doing the same, taking a sizable piece of what later became South Dakota. But this time Congress said no.
**TL;DR:** Iowa would be a better example of a “state that might have been”. Someone should make a map!