[Pelican]

Yeah those suggestions should work. In my quest to improve the MLB expansion experience, I have experimented with minor league teams for the [future] expansion teams, a year (or two) in advance of the expansion draft and the first year for the MLB expansion teams. What works best is adding an independent minor league team for each expansion organization. The trick - as noted above in the other postings - is to "affiliate" the formerly "independent" minor leagues teams with their MLB parents, at the time you create the expansion franchises and set up the draft.

One potential problem is that MLB teams will try to purchase players from the independent minor league teams, if you have that option activated. [And if you turn the option off, it covers your entire sim, so MLB teams won't be able to purchase players from independent leagues like the Atlantic League.].

I suppose in a fictional universe the OP would have no established MLB teams, so the totally independent setup might work more smoothly. You would have to bird-dog transactions between independent teams (or maybe trades by the AI would be okay?).

One other issue I have encountered (in the expansion context) is the amateur draft. I've not found a way to include the expansion teams, in the year before they exist. I don't think the amateur draft can be set up to allow one or two independent minor league teams to participate. Whether the OP could hold a draft with only the minor league teams participating, I don't know. That would be a cool way to "staff" the minor league teams.