The developers actually said that these restrictions are there to differentiate it from the character card/legion system?
Why are they advocating worse user functionality as a feature of the link system, let alone a distinctive one?
That is exceptionally poor reasoning.
-The restrictions on the link system are not the only differences between the two systems.
-Removing the restrictions on the link system does not require giving it the same features as the character card/legion system.
-The link system is a simple system, in which you can apply bonus skills to your characters.
-The legion system is a more complex system. It provides a large variety of stat bonuses and uses a grid + tile system for every character. There's also the boss and coin collection aspect.
-A merge would result in skills being split across 2 completely different UI. Not all link skills are passive either.
If the aforementioned restrictions were removed from the link system, the only aspect in which it would be similar, is in providing bonuses to all characters at once.
That is just better user functionality. Better user functionality isn't something that should be held exclusive to one system over another and it also isn't reason to continue imposing restrictions that have no place being there.
It only serves to make the user experience a lot more tedious for no meaningful gameplay benefit (e.g. balancing).
You've mentioned how the link manager was updated. I am not going to sing praises to Nexon for improving upon a poorly implemented system.
While the updated link manager is much better than its predecessor, they are still imposing unnecessary user-side delays.