Having the Doctor represent an out of date icon of colonial masculinity (traveling around the universe fixing things because no one else can) isn't necessarily a bad thing as long as other characters are there to offer alternate experiences and perspectives. I tend to think that is the purpose of the companion and the supporting cast. There are other directions for the show, certainly, but the existing one is perfectly valid and can even be progressive if used in the right way. I would certainly be curious to see a deconstruction of said status quo as an arc for a season or two before they jump towards changing it too dramatically. Honestly I don't care that much though, as long as the show is well written and well performed with strong characters and interesting stories. That is what I'm watching for.
We saw a black Timelord in "The End of Time, Part Two." Which makes sense. Why wouldn't they have Timelords with brown skin? Hell, the entire idea of race falls apart when the species can change bodies all the time.
Skin colour used to be about the last hundred thousand years our bloodlines spent outside in specific "unchanging" climates. Gallifreyan's, have spent the last hundred million years indoors. Of course different cities might have specifically different static climates, that if your bloodline decides to stay put for a hundred thousand years, then the colour of your descendant's skin is eventually going to be exactly what that city says that it is.
Clearly the genetics of time lords are far different from that of humans or any other form of life on our planet. The standard dominant/recessive traits that result in many of our features seem to be able to coexist in the gallifreyan genome, exhibiting without intervention from other dominant or recessive alleles. I think of it as the genome of an entire population coded into one super genome that is dormant in the time lord until a regeneration calls upon it to spit out a randomly (or less randomly for certain time lords) generated genome for the new regeneration. Perhaps it even has a shared psychic link across the entire population and responds to successful or unsuccessful traits so as to be constantly tweaking the population for the greatest possibility of success.