Hmmm....
If the routes longer, its more profitable, but the merchants don't like it, so its also less profitable, which leaves it just as profitable as the shortest route possible. Here's the Idea...
So lets say a route is twice as long as the SRP (shortest route possible), well lets say the profit would be 10bc instead of 6bc, but because of the merchants not liking it, your route will only go up in value (10bc) every four weeks, instead of every week.
So I'm going to assume that the SRP is 100 parsecs long and the new one is 200 pc long.
Now if I crunch these numbers...
the old one would be worth 600bc when it got there.
the new one would be worth 500bc when it gets there, but it will take twice as long to reach it's destination, wont get shot at, and could go past a few more trade starbases.
And about lenghthening and waypoint maximums. No limit on waypoints, but definetly put a maximum to lenghthening, like 200% or something, and then add about 100% percent for each extra planet (If freighters can go to more than one planet).
They might need to change up the trade managment screen a little (especially if they decide to let a freighter go to several planets)...
1) Like the lines representing trade routes on the mini-map thing should show alterations in the path.
2) And the data thing would have to show all the planets it travels to.
3) And The trade you get from each planet.
4) And (If the freighter go's to several planets) if you declare war (or vice versa) on someone, there should be a button to make the freghter stop going to the enemies planets, but still go to freindly planets, like a "kill sub-route" or something.
Also, if you make it go to several planets, the freighter should have to return home before going to the next planet, because it already sold all its goods from you.
One more Idea...
To stop abuse on trade routes by winding them around trade starbases.
You can only place one waypoint in the influence area of a single econ starbase.
And the path of a single freighter can only pass through a single econ starbases influence area once.
Just some Ideas.