Of course fans will have their preferences. Where the Doctor is concerned they always have. Nothing annoys me more than someone who has seen only the new series deride the older series because it's not as flashy. At the same time, it annoys me when you have some form of Classic Who vs New Who debate. This isn't Star Trek where you have the differences of Old Series, Next Generation, DS9, Voyager, Enterprise, and Star Trek Kirk's Crew 2.0. This is Doctor Who. Sure there have been some changes in the intervening 17 years of the show's hiatus, but change has been an inherent part of Doctor Who since the first regeneration. The content of the stories is much the same as it always was: the Doctor comes across some mysterious threat in his travels and figures out a way to defeat it. Some times the threat seems comparatively small, sometimes it's of universal proportions, but the Doctor rises to the challenge.
It seems rather to be missing the point to completely dismiss the "New" series as not matching up to the "Old" series. The fact of the matter is the older shows were rather hit or miss, as any TV series is going to be, especially one that has over 20 years of running time (with the newer episodes I believe it's much closer to 30). With a show like this, featuring a continuing character from it's inception, the only way to judge it is as a whole.
FWIW I'd say the quality depends on the incarnation of the Doctor (as the actors playing the Doctor seem to be related to the writing staff helming the show). So, we can argue about which Doctor is better, or even rate them (placing Colin Baker at the bottom of the list), but it's pointless to use a New vs Old dynamic, because no matter the complaint about the more recent shows, I can show you the ridiculousness which is the earlier Pertwee years where the Doctor was stranded on Earth.
But regardless, I think we can all agree that the current series is better than Colin Baker, and that even Colin Baker's run was better than the TV movie. And for this we should all be happy.