Totally different type of change. Reducing the damage on an enchanted sword is a legitimate change to make it harder, adding a hunger bar to a brand new game is a legitimate change to make it harder, cool down is a change that only benefits PVPers while making it nearly impossible to defend against 2 endermen at a time or a gang of zombie pigmen, and penalizes a large part of the community for the benefit of the few. It's really not an equitable change.
Well, the same logic regarding making the game harder with the other two works for the cooldown. And this makes PVE better also (I've been playing 1.9 for days now not counting snapshots) forcing the player to focus and take the shot so to speak and...
Bring a shield. This new system relies heavily on shields. The shields last a long time, can look cool with banners attached, and negate attacks entirely when angled correctly. In some cases, they can even negate entirely a creeper explosion.
Pigmen I can sweep to the side even easier than before thanks to new sword properties. But endermen zig zag around and teleport when attacked sometimes avoiding the attack forcing a bar reset, so I see the problem there. That's because you are not properly equipped. Let me explain. Previously, endermen were iron tier mobs. Now, they are diamond tier mobs. Meaning you should have diamond tier to fight them on a reasonable level. Which makes sense if you really think about it. Many players don't go to the diamond tier because the nether and the end would potentially burn up/devour their ultra grindy new gear. Now there's incentive to get to the next tier to even make it to the end.