The Catalyst was making a cold calculated action when it created the cycle. It decided that organic life was valuable and should be preserved, but organic life would eventually create synthetic life in the course of it's development. If organic life created synthetic life on it's own terms, this could lead to chaos and the destruction of all organic life. Not a certainty, but a possibility given the chaotic nature of organics.
The solution that the catalyst came up with was sort of a controlled burn of organic life. It created the reapers to cull the advanced civilizations that could create its own synthetic life and preserve it as reapers. This allowed something of the old civilizations to live on, and new civilizations could prosper.
It's a rational machine mind imposing order on an irrational organic system. Like when we build a zoo and mimic animals' natural habitats in little managed pieces. You have lions and gazelles within 20 yards of each other, but you keep the lions from eating the gazells. The natural order is for the lions to eat the gazells, but, if you do, you have no more gazells.
As anyone who's seen or read Jurassic Park knows, you can't impose order on chaos forever. Organic life was able to overcome the reapers by progressively constructing the Crucible over countless cycles. Shepard is given the choice of how to end the cycle, but the choices all require a great sacrifice.
I think people don't like the ending because they where expecting a space opera ending with dancing ewocks and force ghosts of all you fallen crew mates nodding approvingly. Instead we got a more typical literary sci-fi ending.
Let's face it, the real ending has generated far more thought and discussion than it would have if the ending was Shep and Liara sipping margareetas on a beach.