On my first playtrough, I had the same problem; there were simply too many of them!
Now, on my 5th playthrough, they actually come in just the right amount.
I guess it simply depends on your luck.

Still, there are two problems they had on each and every playtrough...
First, they are not that strong imo, but that's fine since I'm playing just on expert, so I guess it will be fine when I rise it up to master (I hope).
Second (and even worse), they are boring!
They are boring because they are all practically the same!
I mean, check out Big Daddies from Bioshock 1 & 2 (have made a thread about it http://www.gamesas.com/topic/1344681-big-daddiesbig-sisters-or-dragonsdragon-priests/page__fromsearch__1).
Big Daddies are simply so much... more!