Actually, it's not fair to do a direct comparison of UU's when the main interest is (or should be) balance. It's fairly common to tone down excellent civ traits with relatively weaker UU's, e.g. France, America.
I tend to agree that 33% more cost (or 5 shields) isn't worth the movement bonus for a 2-move unit, although on some maps it would be.
The Jaggies were toned down from 10 to 15 shields because the combination with military trait was too powerful for the cost. They're doing the same here, increasing the cost because the synergy of trait and bonus demands a higher cost. In my mind, this is why they also lower Gallic Sword cost to 40. If they kept the Celts Militaristic, I'm in the camp that 50 was the right cost. Lowering the cost to 40 helps the AI quite a bit, and taking out the combo of this powerful a unit with Militaristic is what made it a balanced change. Same reason two best ancient attackers (Immortals and Mounted Warriors) are both with non-militaristic civs.
So if you want to compare Jagged Warrior cost with Chasqui scout cost, the traits must come into the picture.
Aztecs are militaristic and (now) agricultural
Incans are expansionist and agricultural
Conveniently, they're both agricultural. Given a desire to have two 1.1.2 units, they chose to have a lower cost unit for the mil civ and a extra movement bonus for the expansionist civ. Seems a good choice in this light. The point is, that the Aztecs are truly *unique* among all military tribes because of their UU, and the Incans are truly *unique* among all expansionists becuase of their UU. One did not do very well with Aztecs by playing a 'normal' game -- the large majority of players would either whine that the GA was too early and never make any use of the Jaggie, or they would play it poorly then give up on the Aztecs when they got crushed. But in the hands of good players, the Green Machine was an awesome force (witness Sirp's Open SG).
If I wanted to make a prediction by analogy, we'll find that most players will either play a 'normal' expansionist opening treating the Chasqui as scouts (but having only half as much of them), or will disdain the unit and never benefit from them, and it will be an unapreciated civ. Finding out "solid" ways to make good use of the Chasqui isn't as obvious as the Jaggie rush, but I'm betting that good players will make very good use of them.
--- more thoughts in EDIT
Let's consider more the combination of
agricultural and expansionist together, and what implications it has for the Incan opening.
With the extra food bonus for a river capital, there's a new option on the table. Those looking to focus on the agricultural trait of the Incans will go high food, get an extra worker or so early, and get more cities and bigger cities faster. Compared to a non-agri civ, they can probably get to a point of having one extra scout-producing city earlier, and hope that the terrain bonus will let their scouts catch up to where a non-agri expansionist would be.
But with that extra food bonus, the old-school expansionist who wants to get several/many scouts out ASAP has a new option too -- he can choose a forest instead of a grassland and have the same food supply that a non-agri city has. This means 2 extra shields per turn compared to a 'standard' expansionist civ. For a low-shield city this would be 3 vs 1 shield, triple production vs double cost for a big win. More typically, this means 4 shields vs 2 shields, double production exactly balancing double cost for the same food supply. If you have a better starting location, it might be a forest vs a bonus grassland, 1f2s vs 2f1s. Then it's an output of 4 vs 3 or 3 vs 2 shields for the same food supply. There's the 33% price increase over jaggies right there.
Perhaps, depending on the map, a player would go max shield and crank out a handful of pricey Chasqui scouts without getting way behind in food, then switch over to maximum food mode at a decreased scout production rate -- so there's a wide in-between range of options as well. So don't give up on the Chasqui yet.
----
Charis
I don't think the Incans are a powerful civ now, at least in SP. In MP it's another story, though I'm not sure of that. With so many changes here and there, I hope the Chasqui scout will still be of some help... 
But I highly doubt that.
