In fairness to Logopolis, I think it fares better as part of a larger transitional period, starting with the E-Space Trilogy where we learn about the existence of E-Space and that there are fissures into it from normal space, and where the last trappings of Baker's era (K-9, Romana) are stripped away. It then proceeds into the Master Trilogy, which includes Logopolis where it's revealed that the fissures to E-Space are used to funnel the destructive "decay" of the universe's entropy. The Master's persistence in staying alive past death by taking over the Keeper of Traken, and then proceeding to turn the entropic forces of the universe on itself (because apparently the universe is also "past due" for its death without the use of the E-Space fissures) makes for an interesting parallel about staving off the corrupting forces of decay/rot/stagnation when it culminates in Baker's long-serving Doctor regenerating into Davison while surrounded by the new cast of companions. While being conceptually good in context doesn't necessarily mean the resulting adventure in Logopolis is all that good, I think it still has merit and it does stand out as one of the best of the Master's schemes (certainly, one of the Ainley Master's best).
As to "Time of the Doctor"...well, there's still loads of stuff that doesn't work from the past few seasons in regards to the overall plot-arc things even with the context that the Church tries to explain. But I see it as Moffat hand-waving a "no, see, really, all that crazy kooky stuff I dropped all over the place now has an explanation so we don't need to bring it up ever again." So while I don't think the exposition (what little there is) rectifies the plot holes or other issues, I can at least respect that he seemed to bring all that up so that he could then properly dismiss it as a done deal, and if we never have to address that snarled mess again then I'm all for it.
I'm looking forward to the new era...with Amy/Rory gone we've left behind the sitcom-esque antics brought onboard by their pairing. Clara's nice (and rather nice to look at too), and I liked that the only clear plotarc she's sort-of had around her was the Doctor's repeated attempts to understand her origins; it was more sensible and less random than the plotarcs during the Amy/Rory era, though disappointing that it was so heavily truncated, with only a half season to develop. The short time meant that we only really got Clara as a sort of mystery object than as a full character; now that the mystery's been resolved we can hopefully get to see a stronger characterization and better development. Same goes for Capaldi's Doctor; while I liked Smith, I never really got a good sense of his Doctor's character...mannerisms and momentary emotional states, sure, but not much about his drive or personality (which I blame much more on the writing than Smith's performance, since he really did a good job selling those emotional states even with the silly mannerisms). It'd be nice if Capaldi's Doctor gets a stronger, more coherent personality at the same time that Clara might start to get one of her own...hopefully that's not too much to ask.
In the meantime, I'll mention this: Matt Smith had shaved his head for another role he'd taken during a significant portion of the Christmas special, hence the silly bit with him wearing a wig, but it means he's wearing one for the Amy hallucination. And as it happened, Karen had shaved her head for her role in the upcoming "Guardians of the Galaxy" movie (a Marvel movie which ties into the world of the Avengers, though I don't know that the connection will be all that strong or evident). So in that hallucination, neither actor has any actual hair, it's all wigs. Just a funny bit of trivia.