More or less. Colonel (not yet Brigadier) Lethbridge-Stewart debuts in episode 3, but technically the Doctor met him offscreen sometime during episode 2 (which Troughton wasn't in due to being on vacation).
Why they can't do 2D with a static pattern. Most animations already don't do billowing effects or other complex things. The drawn designs might look "too busy"... I'd buy both regardless. Correct. The Doctor does meet Lethbridge-Stewart for the first time. It's not all that epic iconic... After seeing the teaser again (the 3D just doesn't work), I was reading something this AM, where the episode may have been sold to a private collector (or stolen because of the belief of the alleged importance of the "Doctor meets Brigadier for the first time, oooh-aaah-oooh" scene when 60s Who just wasn't into "epic iconic moments" tropes as such)... and/or ended up getting destroyed during transit. Another article/forum had a post suggesting a lot of episodes were destroyed out of the fear of what the BBC might do. Whatever happened still seems to be supposition all around. Either which way, the fragility of these films is still a more significant issue and who would really acquire a reel of decaying 16mm film that they couldn't really use? (Even once, without incurring possible risk of it getting into unplayable shape as a result.) Just sitting there on its side, in visible light or in the dark, will have it rotting anyway and what are the odds the collector would store it vertically in a cool dark place? (And even then...) Regardless if it was sold or pinched or destroyed en route, by now it'd probably be irreparable so it's worthless. Hence the BBC doing the animation. Realistically, new finds will be few and what might be found might not be properly salvageable.
Y'know, considering Big Finish is part of this, and they've got voice actors for both Two (our own Jamie, Frasier Hines) and, now, the Brig (Jon Culshaw)... if I were them, I'd be extremely tempted to animate just one extra scene to give our two heroes that long-overdue actual first meeting. As an Easter Egg, if nothing else.
To be very exact, episode two has an extra in the Colonel's boots looming up behind the Doctor (who is maybe also an extra, because as you said it was Troughton's week off), and in episode three they have already met, so their first conversation always happened offscreen. Something that can never be the same now as in 1968 is that the Colonel is very suspicious. He miraculously survives a Yeti ambush, does so a second time, believes in the TARDIS and wants to retrieve it. Now we know he isn't the Intelligence's agent, but in early 68 he was prime suspect.
That link comes up as dead when I click it. I found a Google cache of it, which I just saved to the Internet Archive (link). And, yes, it's 3D animation. Probably mo-capped and then tweaked. There's a lot of bad in it, like blinks in random places and not where people actually blink.
It doesn't look like motion-capture to me; the movements seem exaggerated, more extreme than a living person's movements would be when they talk. It seems marionette-ish. I suppose it's possible that it's mo-cap of someone who gave an overly broad performance, though.
It's got a lot of extraneous motion which is typical of mo-cap. People move around a lot more than they realize and that's exaggerated when figures are simplified. You can see the same thing happen in rotoscoped live action a la Bakshi's Lord of the RIngs, where the characters often seem twitchy.
Hmm, makes sense. Also, mo-cap performers might be hired based on their ability for dance or mime rather than character acting, which could also lend itself to broad, theatrical movements.
Most mo-cap only tracks surface markers thus is literally superficial, missing the underlying structure (skeleton) and points of articulation. If you don't get the rigging just right you end up with things that are very close to the performers's actions but not quite on the money, so you get an additional level of "uncanny valley" related to movement. This is in part why a lot of mo-cap gets hand adjusted by animators.