If, in EU2 terms, Scotland annexed England, should there still be some sort of Act of Union? This would truly be an odd event, having Scotland dominate the English economy in a reverse of what actually happened, of course. Would the crowns always be maintained seperately by the Stuarts if they had decided to rule from Edinburgh or would they eventually decide to unify their rule?
What would be the effects? I would propose, as a start, to consider the possibility that Scotland would gain the Anglosaxon cultural group but that there would be no gain of any CB shields or other gains.
This would be different from the English version of the event for the following reason:
The northern kingdom did not have a history of regarding their southern neighbors as being of an inherently inferior race. Indeed, historically, "English" and Gaelic culture lived side-by-side for centuries in Scotland (in sharp contrast against the EU2 model that claims that all of Scotland was "Gaelic"--the area around Edinburgh was very Anglo-Norman in culture and had been since the 12th century or earlier). Indeed, the attitude of the Stuart kings historically was neither to turn England into Scotland nor Scotland into England.
Therefore, if there were a "Scotland-dominated" Act of Union, it would likely have a more accommodating result than the "England-dominated" version.