The Catalyst isn't programmed to care for Human, Asari or Turian life, or the lifes of his maker. He is made to care for the survival of life, and it thought the best way of preventing all life being whiped out, is whiping out only the advanced life every 50.000 years and give room for new species to develop. Which is not such a very strange thought, just look at reality, because humans are in control of everything, the other species on this planet have it alot more difficult, they are being hunted, their living space is being taken over by humans, polution, they never get a fair chance with us around.
I don't get why people think the Catalyst is the worst thing ever, it's just an AI that takes the shape of the boy Shepard has seen before, he is NOT the boy. Mass Effect was full of AI's, so it's not that strange that one is controlling the reapers.
The problem I myself had with the original endings is that apart from a few colors, all the endings are the same, it didn't show the results of your actions and it was pretty depressing. In my opinion the extended cut fixed alot of that, the endings are still the same, but you get to see what each ending does, and some things have been made less despressing (instead of your crew being stuck on a random planet, they manage to get off it in the extended cut for example). Although I am still not a big fan of control or synthesis, they are choices, you choose the ending that fits you, for me it's destroy, my Shepard get's to life, the Reapers are gone, Shep's crew isn't stranded so they will meet again, the mass relays and citadel can be fixed, the only downside is no EDI/Geth, but that was a price my Shepard was willing to pay.