I can understand why they made the choices they did with the characterization, and with the off screen time war back story.
If you think about it, the time lords really had been removed from the universe, by the BBC. The doctor himself narrowly survived death by American TV, his fate unknown for a whole re-generation.
It really was a mystery who this doctor was going to be, where he had been, what would happen on his return. So his situation and demeanour was somewhat fitting.
Once the show was a success, they fell on their feet with the next actor, so possibly that was the best outcome.
In all fairness, I don't think with the best will in the world that you can say Davies or Kring were particularly consistent in maintaining their highest quality output every week of the season. Heroes and Doctor Who were both uneven. For an actor perhaps more used to mini series and film, and looking at some of the high end HBO series or even a network rival like LOST, perhaps it just wasn't where he felt the franchise could be at. Remember, there were times when the show suffered by comparison to its initial template, Buffy the Vampire Slayer. In fairness, RTD was perhaps out of his comfort zone with a genre show like this. SM appears a little more literate in what sources to draw from to keep an even keel.
It may be the case the BBC was very willing to make the new show work as a Saturday night flagship, to the extent that a comparable show in the American system, along the production style and schedule they were seeking to emulate, would just get shut down and cancelled if beset by production woes. So the favouritism may have caused the cast and crew to have to gruel it out, as opposed to getting jobs elsewhere. Which paid off in the end. The interview does indicate he was proud of his work, and he identifies with the cast and crew as having been in it together. The criticism, which is not quite visible, seems to be directed at management, logistics, creative direction etc.
Possibly with a two season experience, he'd have a different outlook, and fans would have more material to influence their default instinct as to the natural tone of the new series. Or possibly staying put would have confirmed his reticence about the series. Who knows. But his concerns, which on the face of it seem legitimate, probably owe to having been the lead in what was at times a troubled production, and which without the history of the character, might not have fulfilled a full order of episodes. Perhaps we ought to see the remarks as being coloured by that.