Have not compared the BKK or Pattaya rates, but for other cities, it seems that Agoda rates (after adding taxes) are still slightly lower than Booking.com, or other websites.
The difference is that Booking.com is a reservation website, so you will not need to pay in advance, and pay directly to the hotel after the stay (you still have to provide a credit card number, so you'll still be charged for a no show), whereas Agoda takes payment in advance, so gives a bit more of a discount since it is cash in hand for them.
Previously, the choice of hotels on Agoda was more limited compared to Booking.com, as the major chains were not always represented, but that seems to have changed recently.