Some questions came to mind as I read this thread and thought about the episode:
1. the Master's companion was looking pretty sickly in the last episode. She didn't seem to be able to stand upright on her own, swayed a bit, and there looked to be some bruising under one eye. She also looked vague and malnourished. What's up with that? She seemed like a competent partner ("I already made my choice") in the sound of drums and suddenly she turned into a wet rag a year later?
2. the Doctor tells Jack that he "feels wrong" to him, that there's just something not right about him. But he's never felt odd about the Face of Boe (of course, I suppose that's because they didn't originally intend to have Jack be the Face of Boe, but still..)
3. I'm really glad that Martha stood up to the Doctor and was honest about her feelings and about how he was making her feel about herself. Personally, although I like Martha, her snarky remarks and lovelorn looks would have gotten very tedious after a while.
With regards to the ease of fixing the Tardis - maybe it has something to do with the sentience of the time machine itself, which also seems rather fond of him ("We had to save our doctor"). So maybe the fix the Master would have had to make to the Tardis would have required the cooperation of the Tardis itself - hence the ease with which the Doctor fixed it whereas the Master could only encase it in machinery to force it to suit his purpose.
I think I had something else but I've forgotten already..
/ali