Melee attacks being uninterrupted by flash is counter-intuitive for both sides of the fight
So, I don't know if many people know this, but when you flash away from a guy swinging his weapon at you, it'll still land after the animation is complete even if you're quite a distance away from him. This is most noticeable on Nautilus who I believe has the slowest attack animation in the game. (to be a good Nautilis player you actually have to learn *not *to orbwalk, and to let your attack land where someone used to be before running after them.)
Now, what this often results in is the following: 1. Champion is low on health and flashes out of an intense fight in reaction to the enemy swinging what he knows will be the final blow, and the dies several feet away, punished by his quick reaction time. 2. Champion is about to land the killing blow and sees the enemy flash away, he quickly reacts by stopping his attack animation to give chase, possibly losing the opportunity to have landed the killing blow because he reacted to an "escape"
Now, if you were too slow in either of the scenarios, you actually benefit out of the situation, because something you weren't aware of functioned in a way you wouldn't expect. But if you happen to be able to react this quickly, the result is a humiliating failure for demonstrating skill.
EDIT: To put things into a more easily understandable perspective, let me draw this comparison. Most players learn to be distinctly aware of the wind-up times of powerful skillshots, such as blitz grab, thresh hook, lux/morgana snare, ect. Also, there is a reasonable amount of time where a player can react to such abilities with flash. Your choices in these situations are to use flash or not use flash. If you flash quickly enough, the ability is spent, and you dodge whatever it was you were afraid of. Yes, there is still a chance to use flash and still be hit, or to be unable to use it at all; however this is consequence of a failure to react. You can also choose to not flash, and still avoid things, this is a different form of reaction, and you are rewarded by retaining your ability to flash.
There are distinct player chooses and predictable consequences in all of these scenarios
Now, when a champion is closing in on you in order to melee attack, there are still the same two choices, flash or don't flash. However, in this situation any reaction is a failure. You may choose to flash, and that mean you will use flash and die. You may choose to not use flash, and you allow them to hit you when they might have otherwise accidentally caused themselves to miss.
I'll admit, the canceled your own auto attack when they flashed away scenario is incredibly unlikely. But we as players know it is possible. When we are forced to consciously make the decision to fail, it kinda suck regardless of unlikelihood.