The sequence was meant to show-off the 3-D filming. Though, to be honest, even though I only watched it in 2D I actually like the sequence. It's a fun little bit and exactly the kind of extravagant thing that should be done for a fiftieth anniversary. I say keep it.
I don't hate it, just saying.
Totally. The way I would have done an Ian cameo is instead of Tom Baker's scene have a scene, perhaps in the museum, doesn't matter though with the Doctor and Ian sharing a bench together having a chat. The Doctor recognizes Ian, though Ian is of course oblivious to who the Doctor is. After their conversation is done the Doctor gets up walks away, and as he's walking says something like "see you around, Chesterfield." This gets Ian's attention and when he looks in the Doctor's direction, he sees the Doctor enter the TARDIS, which then takes off. I get goosebumps thinking about it.
My idea was different. See, I think the world needs more Tom Baker, so I wouldn't even dream of cutting that out.
However, after the Doctor's conversation with the Curator, I actually have the TARDIS landing in an office, looking for Clara, only for Ian to tell him that she's not there yet. Then the Doctor and Ian would share a conversation, about how time changes and so do they (Ian could quip about their distinct reverse in looks), so definitely have Ian consciously be aware of the Doctor's changing appearances (spin-off would always cover that field, anyway). Ian might then remind him of his past, their shared past, and the Doctor would reflect on that, tell Ian to tell Clara he'll come by, "say hello to Barbara for me", enter his TARDIS, dematerialize, Ian gets the goosebumps. Then, the end scene as is.
I mean, Tom Baker and William Russell? Now that's almost a proper 50th anniversary, right there.
Including Zygons in Day of the Doctor is fine, the problem is Day doesn't really resolve the storyline at all, it just sort of gets shoved aside as it's being resolved. Indeed, we don't get any kind of proper resolution for another two years with The Zygon Invasion/Inversion storyline, and that I would gladly dump like the turd it was.
At the very least it allowed for the Zygon two-parter to happen, which is maybe the defining Capaldi story. So at least it was resolved, even if eventually.