Why does it just have to be one? There is some speculation about making "a" reaper during each cycle, but then Vendetta says each cycle is somewhat different, with some cycles having one dominant species (like the Protheans) and other cycles have a number of species (like the current cycle). Besides, they never really went anywhere with the Human Reaper. All they really wanted was a rad-looking boss for the final fight. Aesthetics before sense is a feature of the MEverse.
Even if you believe that MacWalt switched things up for ME3, the Human Reaper in ME2 was at the very least going to be used to solve a great problem of the Reapers. It wasn't just reproduction or 'let's make a giant monster'. Any horrific look, as mentioned throughout the trilogy, was more for the sake of psychological warfare than anything else. If they can design things that visually terrify animals/humans/sapient organics, then they might as well - easier to push in the direction they want.
I know there's the whole aesthetic/marketing reasons behind it all, but I don't buy the argument that there was no logical reason behind making husks, Collectors, and the Human Reaper core what they looked like.
Didn't Harby dismiss them as primitive?
True. For all we know, the Reapers had no plan to make any sort of 'capital' Reaper, and were just going to turn the Turians into organic-ish slaves and harvest the rest into smaller Reapers. *shrug*
You're getting your reapers mixed up. Sovy bought the farm two years prior, Harby is now Reaper-in-chief.
I'll always carry my idea that Sovereign = The Catalyst until Bioware directly indicates otherwise.