It's the role of the scout to discover new areas, and look at the second image, there is fog of war everywhere.

And, it's the same for an already discovered area, and even if the full area is completely visible (all area discovered and monitored by sensor ships).

No, he's right.  The ships always take the long route.

I would just like to point out that it is not "the long way" 

the ship will travel the same amount of hexes left -right and the same amount on an angle in either example. In this case you can tell pythagaras to shut it

the only difference is that in the one example shown the ship moves something like 30 tiles left then 30 tiles up & left. Wheras the suggested example would have the ship move 1 tile left and one tile up & left 30 times

This bug is especiially frustrating when you set up a line of slipstream and the ship zigs and zags out of it. Has this bug been discussed anywhere else? 

Ticket:

#NYZ-135-91466 resolvesd?

It's the difference between the pathing algorithm calculating a precise approximation of the direct path or a rough approximation.
The length of the paths is the same but the differences lie in the performance, a precise path probably uses more processing power or memory space or both.
So it's just a question of the optimisation of the pathing algorithm.

/just the humble opinion of an informatics student

Saladman, 

We are always looking to make improvements to the pathing.   Two things -- first the paths are similar in length.  That is, if you count the tiles in screens above, the direct path tiles vs. the one where it seems to swing wide are the same.  The reason that it choose on path vs. the other has more to do with what obstacles the ship thinks may be blocking the destination.    That's not to say there aren't bugs in the system, but that's how's working now.  

In order to do that, you would probably need some sort of path-cost database for each tile to determine fastest path.  That would have to be maintained dynamically as starbases appeared, upgraded, or disappeared, even in mid turn.  Even if there is some more clever way of doing it, it will likely be a lot of computing overhead when you pile up factions and starbases.  I would like to see the pathing get more direct, but I do appreciate the improvements that have been made so far.   I think what I would want for your purposes (and mine) is to be able to set rally points along my superspeed space highway and give a ship a list of rally points to follow in the "go to" command.  This kind of thing could also be used to set up patrol routes, even looping ones, which is a different feature, but another thing I would love to have.

waypoints, yes that would do it. :-}