First, the updates are not designed for their phones. The Android updates are just code. The OEM's have to change that code to make it work with their hardware, so most every phone has its own unique OS.
Second, you're talking about it as if there weren't any upsides to the way Android works. OEM's frequently add additional features to the generic Android code. This allows them to use unique hardware and optimize different aspects of each phone. For example, Samsung added micro SD support, high sensitivity touch screen support a bunch of camera enhancements, a few new sensors, and an IR blaster to their version of Android for the S4. HTC added a bunch of stuff to the One as well. Who's out there adding stuff to iOS? You get what Apple says you get and that's the end of it. There are an extremely limited number of developers working on iOS itself compared to the number of people working on Android. It's even more developers if you consider the bootleg ROM's out there. Those are all gigantic advantages over iOS as far as I'm concerned.
So you get a bunch of major advantages for that one major disadvantage.
Most phones seem to get one or two Android updates, which isn't that far off from how many iOS updates each iPhone gets in two years. They just all happen to fall in the first year of an Android phone being on the market rather than being spread out like the iOS updates. I agree it would be nice if OEM's and carriers supported their devices better and for a longer period, though. I'm not willing to give up those advantages I outlined earlier to get that, though and I think many people would agree with me if they understood what it all meant.