It's like I said before, it isn't like we couldn't all see this coming from a long time ago..... and yeah, especially in recent years (although probably it began with ''School Reunion'' in Series 2), there has been significant franchise creep, making the lines drawn between newer and older material practically indistinguishable (certainly earlier seasons were more stark in drawing the line between the shows, but ''Time Crash'' and ''Day of the Doctor'' were practically the show opening it's arms and saying to all and sundry that it's all one big enjoyable mass that has run from 1963 to today).
I think that was always the intent. Naturally, when the revival series was new and its target audience was largely unfamiliar with
Doctor Who, it was a good idea to keep the continuity references to a minimum so that people coming in fresh wouldn't be confused or scared off by a tonne of references to stories they hadn't seen. So the show started out from Rose's perspective and introduced us anew to the Doctor, revealing his world gradually -- which is just how it began with Ian and Barbara in 1963, and with Grace Holloway in 1996 (or would've been if the movie had had the sense to start in San Francisco rather than with the continuity-heavy opening that was bewildering as hell to new viewers). But once the audience had been hooked, and once the show had built up a mythology and history of its own, it started using more ideas from the old continuity, drawing on the whole history of the character and the world, though in a way that still served the new series and its storytelling. Although in the Moffat era, the continuity nods have gotten to be somewhat more for their own sake, rather more frequent and fanfictiony than in the RTD era.
You see similar things in other franchises.
Star Trek: The Next Generation initially tried to divorce itself from TOS as much as possible ("The Naked Now" aside) and create its own original mythology for the 24th century; but as time went on, we got more and more stories drawing on the original series, with classic characters returning and TOS continuity being referenced more and more, until
Enterprise's final season was pretty much one big exercise in setting up or explaining stuff from the larger Trek continuity. There's also
Star Wars Rebels -- its first season focused on introducing the new main characters and their problems and backstories, and only gradually started making connections with the larger mythos, bringing in Lando Calrissian and Grand Moff Tarkin as recurring characters later in the season, then finally bringing in Darth Vader and
The Clone Wars's Ahsoka Tano in the season finale. So it got one season to establish itself as its own thing before it got tied more closely into the larger whole.
