As a last quick note, I didn't even notice the 18 seconds of non-HD footage in SotF so they did a good job with that up-conversion.
I found it very noticeable as soon as it came on, but thankfully it was very brief and not overly distracting. It made me appreciate the HD footage even more.
I think they've done a really good job with this. The picture is superbly clear and detailed. It must be a monumental undertaking putting these episodes back together again, particularly the pilot, which is twice as long and features pretty much every type of effect the whole series will come to use: warp shots, close-up models, alien spaceships, phasers, holodeck, planet surface, transporters, viewscreen, practical explosions, bluescreen comps. The tiny bit of CGI (matte?) was not noticable at all (I already knew it was there), nor were the minor reframed shots apparent. It looked exactly as I remembered it, just much (much, MUCH!) clearer and better defined. Fantastic work.
As for the episode itself, I still quite like it, it's easily one of the better episodes in an otherwise iffy first season. It's got a little of everything in it and it's very pacey. I must agree with the observation about that sickbay scene being weirdly-placed. It does seem like it was inserted there out of necessity after the fact. You'll notice when Riker radios in that he's ready to beam over, Picard doesn't even acknowledge, he just leaves the room like he would have anyway, giving away that the voice-over was added to the scene and it probably wasn't in the script. The magic of film-making; I love stuff like that.
Sins of the Father was fine. I didn't actually notice the weird cropping issue when watching it, but nonetheless I hope it's something that's fixed for the boxsets. The clarity was equally excellent here, and all the Klingon make-up holds up well under HD scrutiny. The matte painting cityscape looks very good, but when they go in for the close-ups of the council chamber it does start to look like a painting. It's passable, but only just.
I liked the storyline but it's not one of my favourites.
The Inner Light is an interesting episode and something a bit different. I figure they chose it because it's easier to convert with fewer effects shots and maybe they wanted to test the outdoor photography. Well, it looks really good; the brightly lit outdoors scenes (was it actually filmed outdoors?) show up lots of rich textures in clothes and skin. You can really pick out the details. The aging make-up does show its age (ha!) but all things considered it's a very good effort. One thing we did notice was when Picard looks out over the city from the mountain that a straw hat mysteriously appears in his left hand; in the previous and following shots, it isn't there. Whoops! And the typo in the credits ("telelay") is very apparent and should have been picked up on. More effort required for the final releases, I think.
That said, on the basis of picture and audio clarity, I couldn't ask for any better and I'm looking forward to the full seasons in due course.