Strangely the weakest episode of S2 was episode 2 and weakest episode of S3 was episode 1. Both written by Mark. I really loved his The Great Game but since then his episodes have been the weakest of the bunch..by a mile.
This is also always the case in his work in Doctor Who. His scripts are rarely outright bad, but never outstanding either. Just a bit bland. He's often surrounded by far better writers too. He's good for your run-of-the-mill, straightforward Doctor Who/Sherlock adventure that makes for enjoyable enough television, but it never moves beyond that.
As for season 3, I know a lot of people are down on it but I honestly think The Sign of Three and His Last Vow were both outstanding pieces of television. The latter might be the best script Moffat has ever written, even though it's not my personal favorite, if that makes any sense. It may lack the grandeur of earlier finales, but there's a lot of beautiful, layered characterization going on there. Every time I rewatch it (I think I've seen it 3 times) I walk away more impressed. I think it'll be one of those stories that will gain more appreciation when people start looking back on the series as a whole in a decade or so.
I thought Power of Three was outstanding too, and watching it live felt like watching a television classic. I was really surprised to see so many people who didn't like it.
I didn't care for the Victorian Christmas special though. I get why they did it, and maybe it'd be okay as a bit of Christmas fluff, but it didn't work for me (especially considering the drought of Sherlock that followed). It felt like it could have been a great Doctor Who episode, but it didn't measure up as a Sherlock episode. I think my biggest problem was that the character of Sherlock works in the main series because he's really a story, a mythical character living in our world. Benedict's performance shines in that context. In the special, everyone was playing a caricature, and as a result of that Sherlock himself didn't work in that context. He was just drowned out in that entire special by every single actor hamming it up. Watson was great though.
Overall, I get that people want more regular stories with Watson and Sherlock just solving cases, but I just don't think that's what this series is. It was never as procedural as that - the fact that Sherlock can solve any mystery means that the mysteries are never really in the foreground. They all have a clever puzzlebox format (which is always what Moffat excelled at, on Who as well), but it's always there to support character studies on these people. I think that's what makes it stand out, and the fact that the seasons are relatively short really works for that. It's more prestige tv than procedural, and while I totally understand why people would prefer the latter, it totally goes against what this series has been doing since the beginning (although that was the original intent of the show, back when it was still intended to be 6 60 minute episodes a season, and The Blind Banker is a telling holdover from that idea, which is really the only episode that fits in the more procedural style, and is still probably the worst episode of the entire series simply because it feels so standard compared to the rest).