The convenience of not having to learn another interface is worth it to me. booking.com may suck, but the individual hotel's website will probably be less usable in the basic sense of taking more clicks to get a booking done and be unfamiliar. Agoda is no better than booking.com, Google doesn't have enough coverage. So what's the alternative?
I use roomkey.com, and always reserve and email directly with hotels themselves to confirm stay details, as well as secure the lowest non commissionable price.