there are other benefits from colonies than trade income..
Bah, trade income is the one income to rule them all!
Seriously, let's take a look at the cryptic remarks and see what we can come up with.
1) In EU3, colonies (distant overseas, actually) generate tariffs instead of tax/production income. Usually, it is vastly inferior to tax and production, but when you take the correct ideas, decisions, and policies, it is a serious amount of cash. I can't see this mechanic being scrapped, as it helps balance out colonial powers along Portuguese and Dutch lines where they lack substantial territory at home, but compensate with insane tariff income. This is probably still in to some degree.
2) In EU3, colonies can provide range for trade. Pretty sure this will still be in.
3) Colonies (overseas on another continent, actually) enable the use of colonial conquest via QFTNW. If you don't already own a colony in the neighborhood, you don't get to snag other colonies on the cheap. I am pretty sure this will be in given the success of CBs and war goals in other recent Paradox titles.
4) Colonies allow potential access to the bonus for a specific good if you produce enough of it. I don't know if this will be in.
5) Naval range from colonies. Pretty sure something like this will be in given the appearance of trade routes in the game that cover specific sea zones.
So, from this speculation, it seems like the benefits to colonies are still kind of there, even if you don't own either end of a trade route; however, the big colonizers benefit most from constructing empires. Colonial empires will probably benefit from geographic cohesion and economies of scale (i.e. having lots of colonies).
However, if trade routes are static, does that mean there is less benefit to controlling/owning them? In EU3, owning a COT is kind of a big deal for just about everyone because the income from ownership (not even counting the ability to embargo people) is substantial. It's even more important when the value of the COT is absurdly high. And your trade policy in EU3 tends to redirect trade; mercantilism has a big advantage in forcing your provinces to your COTs, where you at least have some advantages (even if free trade is probably better in the long run thanks to TE.)
In EU4, if I own a colony that trades with Spain, but I'm France and big into mercantilism, how does this work? I mean, it's the sort of issue that British colonial policy wrestled with for years before the American Revolution.