I think the enderman mechanic was a good START they just need more to make them scary.
If I recall, Notch tuned them down in the follow-up patch in 1.8, only to buff them up again in 1.9. I haven't done much exploring in the 1.9 prerelease to get a good feeling of how they are after being changed again.
Well creeper's are far more dangerous and are SILENT until they're right behind you! They make me run and jump in shock and all. I hate them ambushing me! Endermen are cool though, I don't mind them and they don't mind me, we can chill together all we want and no one will explode.
At range or groups: Skeles. My first experience with friends on a private server ended up in us unwittingly mining our way into a 3 dungeon 'mega dungeon' with all Skeles. Nightmarishly hilarious amounts of dying ensued until we got our loot.
Solo: Creepers. Silent an they pack a punch. Endermen, the few I've seen/killed (prolly no more than 5 total) seem to be just teleporting Zombie with a stickman figure that (until 1.9) carry random blocks. Not very scary. SSSssssSSSS BOOM! is.....
Endermen are much creepier, but Creepers are more scary practically speaking. Endermen are just slightly more annoying zombies.
Neither of them compare to how threatening a Skeleton is on Hard, though, especially if you aren't on level, open ground and don't have a bow to shoot back with.
This, in 1.8 Skeletons may have an slower fire rate, but their range, accuracy and projectile speed was increase, I got sniped from above so many times while exploring ravine, Creepers are slow and limited to very close range, If you have an diamond sword or Iron sword (with critical hit) you can kill the Creeper without it Blowing up, Endermen in 1.8 is very weak in terms of Health, And you can easily avoid one, just don't look.