One thing FL Companion lacks is the ability to specify a destination and then list the commodities near me or on the way that will make decent profits. For example, I need to go to New Tokyo, I am in California now, what should I buy here or on the way that I can sell when I reach New Tokyo or some station along the way.
Also, on a wholly separate thing, the in-game navigation system is server-side, as are the player maps and base lists. I think the code that does the route calculations can be replaced with a plugin. We need a better one of those. Aeternus might be able to provide more information about the interfaces and stuff.