As Marion mentioned, WikiTree uses the FamilySearch Places API (Place Authority) for the 'bubbles' (location suggestions). See more at Help:Location Fields. Also see the note on that page which states "You do not need to accept any of the place name suggestions. They may not be the ideal way to record the place name on WikiTree. See our style guide below" which states:
Our guiding principle is the same as the one for Name Fields: "use their conventions instead of ours."
Applied to locations, this means using place names in native languages and using the names that people at the time used, even if they now no longer exist.
1. As Tommy mentioned, 1776 is the date that the colonies formally declared their independence and stopped being referred to as the thirteen colonies, but rather the "thirteen United States of America", and is the most recognized date in US History.
So while everything you said may be true, the dates through 1789 are more focused on the initiation of the unified government - while we are focusing on the name itself and what was used at the time.
2. See above again, particularly for our guiding principals on Location Field style, which we "Use the full place name for counties, states, provinces, départements, etc." So while FamilySearch Places is not the perfect solution, it is one that is very comprehensive and would take considerable man-hours to replicate for our own purposes. It is much easier for us to just add the word "County" (or any other missing place designation) as needed.
3. Changes to the system are not directly performed in the database (nor should they be). WikiTree is first and foremost, a wiki, and changing the database directly would corrupt the Change History. The action you are looking for could be performed by a Bot, but would need considerable input and review from the entire community. According to the rules on Bots, there would also have to be an approval for every single action. For instance, changing:
Houston, Harris, Texas, United States to Houston, Harris County, Texas, United States
would have to be approved separately from changing:
Akron, Summit, Ohio, United States to Akron, Summit County, Ohio, United States