1) He has a spell with a longer range than a tower that hurts towers. No one else has anything like this. Riot just lowered the cooldown on it. If this was taken away it would make things so much better.
2) Heimerdinger can use said spell in almost complete safety if he knows what he is doing. Surrounded by turrets and with summoner spells/items to escape, killing a good Heimerdinger requires him to slip up or your team to pull off a great gank which can be hard to organize in solo queue or thwarted by Soraka/Shen in grouped queues.
3) His skill set means he will almost always be right in front of your tower. Attempting to push him back is futile if he has his ultimate up.
4) Heal/poke teams (Soraka, Janna, Kog'Maw) multiple these problems by 100 times. Together they can push straight down a lane.
5) He is free this week. (Not that important but it means you'll see him a lot.)
In my opinion Heimerdinger is just too different from all the other characters. He is playing an entirely different game that is difficult to counter at multiple Elo levels.
I don't like it but maybe that's just me.