My criticism of hotels.com was not so much to praise Hilton, but more so to highlight an important flaw of hotels.com, which is that reward accumulation is only possible if no coupons are used.
That to me means that I need to pay more in order to earn their rewards. I personally prefer to use a coupon for 10% off instead of banking the 10% in hotels.com rewards.
Argument for independent hotels definitely stands in many occasions - but those are the hotels that coupons always work on.