They made a point of not using it in CR until the end, because, as it was stated, Bond hadn't 'earned' it yet. They only used it at the end, when he had become the James Bond we know and love.
It wasn't used that much in QoS, though, either. Maybe one or two places, aside from the closing credits. Though I did like how
it was used, with an unusual arrangement that fit in with the flavor of the track. I personally think the Bond theme should be laid on thick, but also integrated into the score so it doesn't get too repetitive, pretty much the way "You Know My Name" was quoted throughout Casino Royale, but always in different ways appropriate to the mood. You can even have it straight up when Bond's just being insanely awesome.
I don't particularly want to go back to the early days, where James Bond gets his entire theme music straight-up when he arrives in a hotel and starts unpacking his suitcase, but I consider that a far milder sin than one of the Dalton movies I watched recently, where the score was so dull that I was screaming DA DA, DA DA, DA DA DAAAA, DA NA, NA NA NAAAAA! at the TV during an action sequence it should've by all rights been playing over.
Well, that's not too bad. You can have a Bond movie without him. I was worried he'd been recast when I saw the headline.