Caravans seemed to be one of the most hated things from WoM, and so they were removed in .86. A lot of people consider this an improvement but really they have simply removed trade from the game entirely, adding to the two dimensionality of the game. Which is a shame because although caravans were done badly they had a lot of possible depth.
The new system is good in several ways. It allows players to create roads without any micromanagement, instead of having to move a caravan to every city you just research a tech and baam roads connect all your cities. Also there where too many caravans wheeling around in the other system but now the number of caravans has been greatly reduced. This is a definite improvement. This new system is flawed in several other areas though.
First of all the only way to connect to other factions is through a economic treaty. This creates a road and caravan between your capital cities. This isn't a bad way to connect civilizations but it has problems. The economic boost is negligible it's all about the road. In fact the main use of this treaty is for invading the other player. It paves a road right to their capital so you can march your army right into their territory. The AI doesn't seem to realize that I am not offering an economic treaty out of friendship and good will. Why even bother with the caravan at all. It's just a small gold multiplier in your capital. The trade treat is just the same thing but to overall gold output.
Caravans themselves are negligible. They can only connect to you capital so, except for the fact they have no cost or downside, unless you are running a gold heavy capital there is little point to getting them. Without some way to connect other cities caravans are pretty pointless and may as well not exist. It's not as if there is any real incentive to attack or protect them. They seem to exist just to look cool as they move between capitals.
Finally I can think of absolutely no way to add depth or strategy to the current system at all. As long as the only cities affected by trade are capitals trade will never be anything more then a vestigial little gold bonus. I hope the devs take a look at re-adding some depth to trading, or just remove it completely.