I had the same thoughts and didn't really get it but a few it started to fall together a bit when I thought about it a bit more and broke it down into the individual actions the Reapers take and saw if I could tie it all together.

Why destroy all life over and over again:

I'm sure this point will be fully clarified at some point in the final part of the trilogy, but my guess would be they came out on the winning side of a long past conflict and this was their solution to always stay on top.

How do they decide when to wipe out all life again:

Looking at the various races it seems the older, longer living species, have the strongest biotic abilities. From the sound of it only the Asari and a few rare Krogan are naturally biotics, most other species only gain biotic abilities after exposure to Element Zero. From what we saw of sovereign with the indoctrination, and Harbingers control of the collectors, it would seem that they have abilities that would be beyond even the scope of their technology. So the only likely explenation is their using biotic powers.

Why build a new reaper:

After sovereign was destroyed they were basically trapted in dark space, so it would seem they needed a new actual reaper to open the way for their return, as the collectors alone couldn't do it perhaps. This obviously failing the reapers awaken and just take off and fly in from dark space the old fashioned way. Obviously this wasn't their first choice, and i'm sure the expended energy will keep them from being at the top of their came from the very start, and they also won't have control of the mass relays since they never took the citadel.

Why design a human reaper:

The most common reasoning most people agree on, other then the shock factor, is that since shepard was a human and he caused the destruction of sovereign then humans were the superio race to design themselves off of.

What I also think plays a roll in it all though is that even from the start with the collectors plague not effecting humans we are shown that humans are different then other alien races. I believe it's stated that humans have a more diverse genetic background so they didn't engineer the virus to affect humans, and perhaps this makes them the ideal candidate to form a reaper out of as it makes human goo the easiest to work with.

Again going back to the idea that the reapers want biotics, I think it would then be believable that for a reaper to be as powerful as possible the would need to combine both organic and non-organic traits. You mix the organic side to gain the biotic abilities such as indoctination, and the non-organic side in the form of highly advanced technology.

As for the form of the human reaper, I don't think what we saw is what the final form would look like. Looking at concept art for Sovereign it showed that the bottom of the ship actually more closesly resembled the face of the original species thought to be prothean. The tenticle face and all, but then the collectors being evolved from protheans and it being stated they couldn't be used to form a reaper, it could be sovereign was based off of a different race, or that all reapers get the same outer top shell so that they would appear somewhat similar regardless of what race they come from once fully developed.

What will they do now:

I think from the end of ME:2 it's clear that the reapers have given up on gaining control of the citadel and the mass relays after suffering defeats in both ME:1 and 2, and will just fly straight into the galaxy from dark space.

This is probably the only reason that organics will stand a chance in ME:3. As many reapers as their are, and as advanced as their technology is, they will still have to face opposition in a way that is completely contrary to their carefully laid cycles that they have repeated for so long.

Anyways, Just a few thoughts. I hate when I don't find a story point believable in an otherwise good story so hopefully they bring it all together in a coherent mannor. If not then I'll just go off of my own little story I guess!