I think the issue is not with diversity itself, but the way in which it is represented. Everything is being made such a big deal out of these days. I remember the days of Captain Jack, who was quite obviously gay, but it was never a case of trying to score any moral points. This season so far has lost the fun element to the constant moral lecture and trying far too hard to tell the audience how they have to feel about certain issues.
Tennant and Smith's characters were both deeply flawed (I stopped watching for a while when Capaldi took over), but it was often left up to the audience to interpret their sometimes questionable actions.
It feels like now we don't have that choice anymore.
Minorities are also minorities, because they are, well, less frequently present in our lives than the majority. Say, for example, 15% of the population are gay - then I would expect them to be represented in abut 15% of the characters in the episodes. Now it feels like they make more like 30%. That's an exaggeration, of course, but that's the point I'm trying to make.
Dr Who has lost its fun element to the preaching and lecturing, which, sadly, destroys a lot of good entertainment these days. The times when we could look at ourselves in a lighthearted way and even poke fun at things (a lot of humour is built around being politically incorrect) are slowly dying and are leaving a dreary world behind, where fun is fraught with too many hurdles.