Colonial nations should feel a greater urge to go independent and go to war, towards the endgame.

Dynamic appearance of cultures in the New World, based off the culture group of the coloniser.

Ships travelling in the open seas pre-Carrack should suffer massively increased naval attrition. While they would perhaps be faster than in the base game, early (sub. level 4) ships should not be survive in the open sea. Fleets comprising of transport ships should not be able to survive

Terrain should still have the potential to be left by lategame. Harsh weather events, drought, famine, unfriendly natives, and a lack of preparation (for countries with fewer colonies / less familiar terrain (Derien cough cough)) should be able to to die.

If you are nation that has not abolished slavery then there is the chance of slave revolt which can lead to independent nations forming.

Colonies should fully developer ~200 colonists

Native policy should have greater effect, with more events depending on policy. Possibly also make it easier to change policy, i.e. when a ruler dies/is elected.

Co-existance: Good early game, bonus to settlers to stop them dying. Is harder to develop too much though, as the natives are in the way. Maybe resulting culture is that of the natives, rather than coloniser's.

Trade: Increase production, good middle game.

Repression: Good late game, much higher rate of native uprising but faster colonisation rate

It would be good for more nations to be involved in colonisation. Historically minor nations got involved, even the Duchy of Courland.

European powers used manufactories as locations to trade with natives. Smaller provinces with bonuses should model pre-Scramble trade with areas such as Indonesia and Africa

You should be able to have different policies. Plantation, Migrant, and Prestige colonies should differently model the nature of a colony. Plantation colonies should increase slave revolt risk for example, and have higher maintenance

Colonies should be easy to start (sometimes without any direct player input), but hard (expensive, time consuming, and attention-whores) to finish

Colonies (especially Silver) should be vastly more profitable than they currently are. While it should take longer to ramp up production, they should also produce far more. Influxes of silver completely devastated Europe through silver and the mercenaries bought, and this should be modelled with the first colonisers able to enjoy rapaciously tearing through rich central Americans, and being able to import that same devastation home as they fund foreign wars and repeatedly bankrupt themselves

Currently there isn't much difference, and there is no reason not to go suppression. Make it sure there are advantages to trade and co-exist with the natives, as they are the ones who know how to live there.

Native natives should be stronger, with more of an ability to resist the European incursion. In some games there should be a chance that the now more numerous natives are able to resist the influx of European diseases, giving them a head start when it comes to reforming.

0,0,0 development provinces are /not/ colonisable. Surround trading posts and the coast of Africa (and sections of indonesia). Lategame Europeans and advanced African nations should get an event which boosts the development of neighbouring 0,0,0 and sub 4 dev. provinces to allow them to colonise.

With Bartholomew Diaz able to discover the Capein 1488, it should easily be possible to /explore/ far further than presently allowed. What should be limited is the range at which the Motherland is able to exhibit strong control over the colonies.

Colonies further from home ports (i.e. cores) should be increasingly frahile - while you could easily discover Indonesia by 1520, you shouldn't be able to colonise it til far later when your network has caught up

Towards the end game, there should be more events catering towards moving to America. Colonial policies which can unlock later, such as "Penal Colonies" or "A New Life in the Americas" or "Mass Importation of Slaves / plantation colonies" should increase the events and growth in development of certain provinces, such as centres of trade and high production areas.

There is no foregone conclusion when it comes to who had the most developed trading provinces. Nations within a trade node should be able to compete by investing in their colony (edicts? events? advisors? military might?). Estuaries and Bays should be more common, but it should become increasingly hard to gain control of the Entrepot. Control of a key port (i.e. new york, singapore) or the equivalent should be hard, and getting there should be risky