I wonder how much is to do with the change in writers. The 'first' series was written entirely by fans, and fan discourse at the time was that excess continuity killed the programme back in the eighties. Perhaps more to the point, the writers had mostly had their fun playing with at least some of their favourite toys from the Doctor Who box in the novels, audios, comics and (in one case) a Comic Relief special.

With season 'two', Davies brought in a load of writers from outside of fandom who were writing based on their memories of the seventies version of the programme without knowledge of arguments in DWM about whether The Trial of a Time Lord killed the series, or whether epic arcs about Time Wars were rendering the books unreadable.

One other point: it just occured to me that the Judoon are sort-of returning monsters now, if that brief cameo in The Stolen Earth counts.