About trade:
The trade rules I suggested are obviously very vague and just that, a suggestion. Overhauling everything is not a top priority anyways; the first thing to do is boost a bit further the game stability and comfort, and the second one probably relates to the AI in some way.
The advantages of what I suggested was that commodities could have a different price in different regions -- obviously, furs would be much less valuable in Québec than in Madrid, and Europe's main exports would be weapons (and beads). This would allow the players to make a profit from the trade routes. (Think of Machiavelli: Merchant prince of Venice, for those who have played it). If we want to keep things historical (there is an If, there, and a big one at that) there should be no need to actually control a province to benefit from its trade, and a TP could even be set up in a non-controlled province: for example, the Portuguese, and then the Dutch, did a lot of trade in Japan; the French kept several TPs in India after the Seven Year's War; they also had a deal with the Ottomans. The closest we can get to this stuff right now is the trade agreement, which is meaningless if one or both sides don't have a CoT.
So the very rough ideas yield something like:
* the CoTs could have « ranges » much like they do now, and goods would diffuse from the provinces to the CoT to the provinces in their ranges in the same way they do now -- but also backwards, from the CoT to the provinces, from imported goods. This should set up a basic offer and demand economy, without there being too much micromanagement. (In reality, this should be done in a per-province basis, but this is not feasible).
The mercantilism slider would also have an effect on the shape of the CoT ranges: mercantilism would hinder provinces getting access to a foreign CoT (taxes).
For example, now the price of furs and tobacco is controlled by the promotion of civil servants. With this proposal, the promotion of civil servants in Spain, would raise the price of furs and tobacco in the Andalusia CoT only.
* merchants would link two CoTs. An interesting effect of enough free trade would be to allow a greater number of roads that connect two non-owned CoTs (again, the Dutch), whereas mercantile nations (Spain) could only link two CoTs that they own, and nations that fall somewhere in the middle could link an owned CoT with a foreign one. But you would benefit from owning the CoT (Dutch Batavia was set up for this).
* possibility to set up a trading post in a foreign-owned province. (Venice should have one of those in Constantinople at the beginning of the game; France in Pondicherry; Portugal in Nagasaki; England in Hong-Kong). This should entitle you to the trade benefits of the province, and there should also be some kind of counterpart for the province owner (who would obviously benefit from the TP to be in his province vs. the neighbouring one); for example, this might require a trading agreement, so that the province owner can freely trade in the TP-owner's CoT; and this should also imply a diplomatic guarantee.
* privateers on a province would yield to their owner some part of the trade throughput of this province, and a chance each month that the trade route stops (merchant killed). They would also randomly give CBs on their home country for their sometimes uncontrolled exactions (think of pirates sacking Cartagena).
* Mercantilism, while preventing foreign countries to trading with your spice-rich colonies, should also expose you to loss of income from contraband. So the penalty should be in terms of trade efficiency, not in number of merchants and colonists. (Spain was heavily mercantile and still a heavy colonizer; Louis XIV's reign was the times when France was both the most mercantile and the greatest colonizer). This would be an option for a player who is a bit lagging behind in trade, and who would want to be insulated from world trade -- try and hurt the others, even if he gets hurt too. (And this penalty could be negated, for some particular foreign player, by a trade agreement, such as the Spanish Asiento to England, which would obviously benefit England most; or the trade agreement between François I and Suleyman the Magnificent, both at the head of otherwise quite mercantile countries). Actually, this becomes a viable alternative once your part of the world production is larger than what you could expect of the world trade. (Spain, pre-1763 France, early Ottoman Empire).
* A lot of those conditions should be available as peace treaty options. Most peace treaties actually did include that kind of provisons, the Spanish Asiento being the most famous example.
Again, this is by no means a complete and definite proposition, but instead just a basis for more improvement!
Colonies
About the Tordesillas rules: I actually see no reason to make them different from claimed territory. The Tordesillas treaty was weakly enforced and sometimes renegociated (Spain and Portugal did some realpolitik), and grabbing of foreign colonies and TPs was certainly not done via Papal authority but by brute might (mostly against the French, at Fort Caroline in Florida, or in France Antarctique in Brazil). If the Tordesillas treaty did nothing but adding some huge claimed territory for Spain and Portugal, they would get a colonial-CB on anyone settling those places, and would be quite sure to win a colonial war in the early centuries; this initially huge advantage would later be eroded as the navies get mightier, and there would probably be no need for a such brutal ending to Tordesillas as the Tolerance edict.
And just for fun: give the colonies (viceroyalties) some names! Having on a map such separate entities as « Viceroyalty of New Granada », « France Antarctique », « New England », « Dutch East India Company (VOC) », « Portuguese Brazil », « Viceroyalty of Peru », « Danish India », « Louisiana » etc. would be veeeery coool, even with no effect at all on the gameplay.
If it has any effect, this could be related to the core provinces: for instance, « New England » would get cores (by event or by player's action) on « New Netherland »'s provinces, which would yield a colonial war between England and the Netherlands, limited to those colonies (though other colonies *might* get a CB on the attacker too -- colonial solidarity is not a given, but this is a nice pretext for grabbing some extra territory). In some way, this amounts to treating colonies a bit like super-vassals.
Another, nice side-effect would be to help a bit in colonial wars: as the colony already includes some provinces, this is a nice « plug-and-play »revolter.
Again, like everything I said about trade, this certainly poses lots of problems that I did not see.
But even without any gameplay effect, named colonies would really be coooooooool.