I think you are somehow right while otherwise not. It is true that in the first two Craig-movies we see a fresh and new Bond, who is eager to get into the action and is maybe also driven by a bit of a juvenile arrogance (and passionate vengeance in Quantum of Solace). And yet in Skyfall we see a mature Bond who might still not be really grown up emotionally but who maybe has found the routine in his job (and is even a bit fed up with it), and we don't have to forget that it really is an exhausting job that might let you get old quite fast (and "00s have a very short life expectancy" anyway). And in the end he already had to make a carreer before becoming a 00, but I think it was rather the 90s when Silva worked for M in Hong Kong (though not with Bond, they didn't really know each other before).
So yes, he indeed shows some signs of aging and boredom (for lack of a better term), yet this doesn't necessarily mean retirement but merely maturity and getting used to his job. It thus prepares the ground not for the 3rd, but the 2nd act of his carreer, as the last scene of the movie emphasizes, when he is more ready to go on than ever before, actually strengthened by his past experiences (which also suggests that maybe M, being kind of a mother figure for James, actually had to die to further his development). The beginning of his carreer might be gone by the third movie, but this certainly doesn't mean that the end is immediately near. The ageing theme of the movie doesn't contradict the rebooting, but just extends it by a more dynamic development of its main character, more so than all the previous movies of the whole franchise did. We're thus not going to see an old Bond in the future movies, but a grownup one.
This also fits together with Skyfall's ambivalence of on the one hand continuing the modern rebooted line of the first two Craig-movies, while still going more into traditional Bond directions. It introduces classical characters, like Q and Moneypenny, while at the same time adapting them to the modernized line of the reboot.
In the same way MI6 is constantly depicted as (or accused of) getting old and useless now the cold war is over and Bond and M being relics of the past. But it are those old strengths that are needed to win against Silva who comes, like Bond, from the "shadows" of the past and is, with his madness, his desolate island he just "took over" and his whole attitude, more of a good old Bond-supervillain than anyone before him in the reboot. And indeed this is even emphasized by M in her speech before the court, when she says that
Our enemies [...] do not exist on a map, they're not nations, they're individuals.
And those individuals come from the good old times, like Silva and Bond. And this whole theme of reinvention of past virtues is both emphaszed by Bond travelling back to his own past in order to fight Silva on his own territory (and what could be older and more conservative than an old mansion in the Highlands) and this with the goold old DB5, an obvious nod to the old movies.
So at the bottom of the line you are right in that there is an obvious theme of aging of Bond (as a character but also his movie-franchise), while it is on the other hand emphasized that this old-fashionedness is what makes him different and thus a chance to use at his advantage and that both Bond and his movies should, while keeping at pace with modern developments, still not hesitate to remember their traditions. And what could emphasize this more than the overly nostalgic ending scene, which is both new in light of the reboot, but more old-fashioned than ever before when seen in light of the whole franchise.