It could be nice to enable a collect mission (similar to what would be like a self-attack but without any kind of battle, just grabbing resources).

For instance, if a player wants to collect into planet A, he would have three options:

Have cargos in planet B and deploy from B to A.
Have cargos in planet B and transport from B to A.
Have cargos in planet A and collect from B (which would have a two way travel, from A to B, then grab all resources, then come back from B to A automatically).

Is there any particular reason this is not implemented? I mean, are there clear problems this would create?
If not, it would be simple to add, it would not take any space from the user interface, just substituting the Attack button when the planet is from yourself.

Addition: like in attacks, may be with Commander (or other officer) one could modify the order in which resources are collected, or even tell the fleet to leave some resources at planet B.

I don't think this would “create” that. We can already do this. And also, that's not really ideal since you wouldn't have cargos in every planet for an urgency. I don't think that's really a big problem.

And, as you say “the actual way is okay”, yes of course, and “I don't see that it's necessary to have a feature like this”, yes, of course it's not necessary; but if it doesn't harm the game and adds some flexibility, why not include it?