Colonial Maintenance: If you have 10 level 1 colonies, you're in trouble. This slider can be seen in the budget screen, and the more 'growing' colonies you have the more expensive it is to keep them growing at full rate. So it's usually better to focus on one or two (or more if you have the budget) colonies at a time, until they reach 1,000 and start earning you money, before planting more.
Maneuverability: I've always hated having tons of islands because at war you will be highly dependent on moving your few soldiers around with your navies. So, and this is more a style thing, I prefer keeping my colonial possessions in one or two big chunks, on mainland America.
Expansion into New World states: Sometimes the best way to establish 'colonies' is to take them from the natives. A colony at central America (Panama/Choco or Honduras) gives you a nice place to put your soldiers from which to attack Incas or Aztec/Zapotec/Maya.
Mudcrabmerchant: It is a half-point of morale. It doesn't seem like much but lots of these little modifiers can really give you an edge over enemies. Consider it, that's half of Military Drill, which is a national idea. If you had both military drill and Shiism, that's 1.5 morale bonus. In the early game when morale is around 2-3, that's huge.