Gatiss and Moffat have similar problems with their writing. They try too hard to be cleverer and end up with something that doesn't work out when it's actually filmed. And they both like the whole "if you believe/love hard enough, then the monster who is programed to blow everyone up will instead save the day" plot line that has been used so many times during the Moffat era of Doctor Who. It's no surprise to me that they enjoy working together.
On the whole I prefer Moffat's writing over Gatiss's on Doctor Who. (Moffat has written some episodes I love, plus some blah ones. Gatiss has written some of my least favorite episodes, and a lot of filler.) On Sherlock I don't know whose episodes are better… I don't think I've paid that much attention to who wrote which ones. (But I do absolutely love Gatiss's portrayal of Mycroft Holmes.)
I don't think I've ever paid attention to Gatiss as a writer on anything aside from Sherlock, but admittedly I only paid attention due to disliking Moffat's style. I think they usually wrote together on Sherlock, so it'd likely be hard to tell.
Agreed though that Mark Gatiss made a wonderful Mycroft. His ability for portraying microexpressions was definitely impressive in that role.
Other than Moffat writing lines for say a dramatic psychopath, his writing usually reminds me of a college student adding extra words to a paper that a professor told him it had to be at least so long. Maybe Gatiss also does that, but no clue. The feel goods will always triumph theme has annoyed me in some Who episodes too.
I suspect them each trying hard to be the more clever one only helped write the script between Sherlock and Mycroft, but I can see how it wouldn't nessecarily work for Who.
On a whole, I loved the show, but the last episodes I felt were somewhat meh other than the last episode. I think they must have wanted to put all they had for the end.