To fix the problem where people can win the game, with a small number of colonies, in a short number of turns, I suggest the following enhancement:

Have there be an optimal number of settlements. And if you have less than the optimal, rebel sentiment is reduced by a percentage per settlement, and if over the optimal then it is increased. This optimal number would vary by difficulty level and map size.

The rational for this would be that the smaller you are, the less likely your people would revolt, as people have closer ties and dependencies to the home country, but once you reach a critical mass/size, more nationalistic feelings kick in. This would also provide incentive for players to build nations.

An example would be, say for a Standard map and Conquistador difficulty, the optimal settlement size would be 5. For each settlement less than 5, overall rebel sentiment is reduced by 5% (to a maximum of 20% for 1 settlement). For each settlement over 6, rebel sentiment is increased by 5% (with a maximum increase of 25%) so you would reach maximum at 11.

The optimal numbers would need to be tweaked and playtested but I would suggest as a starting point:

Standard Map Size:
Pilgrim = 3
Pioneer = 4
Explorer = 4
Conquistador = 5
Governor = 6
Patriot = 6
Revolutionary = 7

Adjust for other map sizes Tiny -2, Small -1, Large + 1, Huge + 2.