Personally I loved a lot of the themes of the episode but I've already read things from some who didn't. As someone who doesn't ship anyone I thought they were interesting...
Firstly, Martha's arseyness about Rose. Liked that she finally got pissed off with him about that. Yes she's crushing on the Doctor (and frankly, who wouldn't?) but I don't think she loses much of the her strength by doing this. She's not emo pining and I was glad to see her get a bit annoyed about it, especially considering she'd just found out that he has a habit of abandoning people.
Secondly, the Doctor's reaction to Jack. Personally I would have been so disappointed if the Doctor was really pleased to see him. After all he did abandon the guy in the future on a derelict space station full of dead people/dead Daleks - there must have been a reason for that. I know the Doctor/Jack shippers probably aren't best pleased but I loved it. I've always liked Ten as a harsher, harder Doctor and I think that makes sense with his war veteran status. What he's seen over the last 900 years or so has had an effect on him after all. The reasoning for why the Doctor didn't like Jack was so interesting and tied in very well with previous parts of the series (and the scene was excellently played by the two of them). It has been mentioned in numerous episodes before that everything has its time and everything dies. It's the one constant in a fluctuating universe. Jack is now breaking an unbreakable law. He is unnatural. He is just wrong. He shouldn't be. It's not as if he's extremely long lived like the Face of Boe (and omg did my mouth drop when they made the revelation about the initials - glad to see confidential says we're not done with Boe yet because like the Doctor himself said, he's text book enigmatic) nor is Jack immune to ageing yet is still able to die by other means. If he dies he comes straight back to life without regard for the basics of existence. That is totally screwed up. Even in the most chaotic and complex systems there has to be some constants and Jack is ruining that - no wonder the Doctor is so uncomfortable. He's very aware and in tune with the constant fluctuations of the universe, he's used to things changing. To him Jack is like a completely still piece of driftwood on a raging ocean. It makes utter sense that the Doctor can't just get over that - it is wrong on such a fundamental level. His presence is like a disturbance in the Force.
I also think that it lays the ground for Jack returning to Torchwood. He said in the episode how much he'd missed his life with the Doctor. Jack is an adventurer after all. He's more alive in this one episode of DW than he was in most of Torchwood. But if the Doctor feels that uncomfortable with Jack being around then he's not going to let him stay even if Jack would prefer to. And I think he would stay if given the choice which leads me to my third point - Jack doesn't like his Torchwood colleagues as much as some would like to think. I got the feeling throughout most of the series that he wasn't particularly close to any of them. He kept himself separated from them. The biggest exception to me is Tosh. Not in a romantic way but more a friendship/sibling way. They seemed to have a good thing going and by the end she probably knew more about him than anyone. With the others though (and yes that includes Ianto) he kept himself rather distant. I think this was done on purpose on his part - firstly he knows he's going to outlive them so doesn't want to get too attached and secondly he knows he'd drop them like a stone should the Doctor turn up. Which probably doesn't sit well with the Jack/ianto shippers out there but what the heck, I've always preferred to see their relationship as screwed up anyway. No 'happy ever after' for them. I'm still hoping that Ianto is playing him because otherwise his character has been butchered (going from 'I hate you and I'm going to kill you emo' to 'let's forget my pain and shag' without any explanation doesn't sit well with me - either he's got a motive or he's really poorly written).
So all in all, I liked the darker, not so friendly parts of the episode and the way it didn't always paint the characters in a good light. Interesting stuff.
Also kudos to Jacobi but mainly Simm for making me actually like the Master. What I remember of him in the old series made me half dread his return. He just seemed a bit embarrassing looking back at it now - too pantomime and camper than a row of tents. Jacobi was good in his little bit (although I'm not convinced I could have taken many episodes of him for some reason) but Simm's wide eyed crazy hit the spot perfectly. He's a nut, he's malevolent, vindictive and strangely charming in an evil way. Looking forward to seeing him next week.