In the 6th season, I actually liked "Schisms", although the story ultimately goes nowhere. But the opening with "Ode to Spot" is one of the funniest moments in the entire series. I had some issues with the first batch of episodes when I first saw them, but I thought the season got much stronger as it went along.
Essentially, the 6th season started as a direct response to all the family episodes they'd done in the 5th season. Even at the time, Ronald Moore acknowledged that Season 5 had too many episodes that were a formula of A story with the child of the week and B story of "ship in danger". He even called Season 5 the "Year of the Child". At the beginning of the 6th year, Moore and Braga openly stated that they wanted to do higher concept shows that would really play up what they could do in a science fiction setting. Hence you get the transporter creatures in "Realm of Fear", the Dyson Sphere in "Relics", the subspace creatures in "Schisms", Data's information infecting the Enterprise in "Fistful of Datas" and even the third or fourth iteration of "Measure of a Man" in "Quality of Life". It's around "Chain of Command" that things get really interesting, and really good, for much of the rest of the year. "Chain of Command" is a truly great episode. "Ship in a Bottle" is another great one - and a really sly twist on a high concept story. I haven't seen "Face of the Enemy" in years, but I remember it being good. "The Chase" is classic Star Trek mythos. "Frame of Mind" is brilliant. "Tapestry" is a great personal story. The Data story in "Birthright" is a brilliant concept. "Timescape" is good trickery for its first three acts. And "Descent" has one of the best teasers they ever did. That's frankly a lot of good material in one season. It's too bad they couldn't follow it up in the last year.
I actually still have on tape the 25th Anniversary special from fall 1991, as well as the "Journey's End" special. I haven't watched either in 20 years. I remember William Shatner's appearance on the 25th Anniversary special where he had to follow up some clips from TNG and his disdain for it is hard not to miss. The big thing I remember from the 25th Anniversary thing was the promotion for Star Trek VI. I never saw the MTV special.
Ron, you've noticed the change in Troi from first season to sixth, right there. I would argue that she might have lost a bit more than was best, as she looks a bit gaunt in some of the episodes. But that could also be the heavy makeup, which is abundantly visible in HD.
BTW the makeup on James Cromwell's "Jaglom Shrek" in "Birthright" looks incredible in the new transfer. That was a heck of a makeup job, no question.
Another thing - on the commentary and discussion of "Chain of Command", Ronny Cox and the rest go on about how much of a villain everyone thought Jellico was, when he was more of a tough captain with a short temper. I agree with Cox that Jellico is a much more heroic character than people think of him - but he's missing the point. He was hired BECAUSE he had been playing roles like Cuhagen and Dick Jones at that time. They were giving him a Starfleet character with shades of the bad guys he'd recently done. Which makes Jellico a more interesting character, and one I wish we could have seen again at some point. On the other hand, it may be a good thing he was only seen the one time - he was in a great episode, made a great impression and we move on. And the other thing is everyone talks about how much of a contrast Jellico was from Picard. They forget that Picard was a pretty tough cookie during much of the first season of TNG. Remember that in the pilot, his first scenes with Riker are quite tense. He doesn't even turn to acknowledge him on the Battle Bridge when they first meet. It was only over time that Picard began to loosen up - particularly during the third season where Patrick Stewart flat out told the writers that it was boring to just sit on the bridge and receive updates every week rather than doing anything more substantial. That said, Picard continued to have an ability to call the other characters on the carpet in a big way throughout the series - including Worf in "Reunion", Wesley in "The First Duty", Riker in "Pegasus". The pattern there is that Ron Moore wrote all those episodes and he has openly stated that he loved writing "the dressing down scene". I think it must be something in Moore's cadet past that he always wanted to see Picard ripping into these guys...
Comparing the first and the last season of TNG is kind of painful. The final season has the characters in the modes with which we remember them - albeit in some combinations that really didn't make sense. The show doesn't feel particularly stiff. But there's so little of interest during the year that it really feels like they were marking time. If I were to try to look for the quality moments of the final season, all I'd have would be "Lower Decks", "All Good Things", the B-story of "Thine Own Self" and a few wild moments in "Parallels". That's not much to speak of.
If we look at the first season, things are a LOT stiffer and less comfortable. The characters don't really grow into themselves for much of the season, and even then there's still a lot of growing pains. Following the pilot, the camera work doesn't look nearly as good as it would under Marvin Rush years later. And there's a bunch of episodes that are cribbed from earlier generations of Trek. Q is obviously a version of "Trelane". Riker and Troi are new versions of Decker and Ilia. Data is a new version of Xon from the Phase II plans. "The Naked Now" is "The Naked Time" done again, and they practically say so in the middle of the episode. Some of the episodes are frankly difficult to watch - like "Angel One" and "Lonely Among Us". But the first season also has a number of good episodes sprinkled in there. "Where No One Has Gone Before" is the first time I began to feel comfortable with the characters and it felt like they were starting to become comfortable with themselves. "Haven" is a good character episode - ironically directed by Richard Compton, who had played bit parts here and there on the original series and I believe was a friend of Roddenberry's. Around the episode appropriately titled "Coming of Age", things actually started to really pull together - and it's at that point that the first season went on a run of stronger shows to finish out their year.
To wit, "Coming of Age" is a great summation of what they'd been doing so far and had some great character interactions with the Remmick interrogator. "Heart of Glory" is still one of the best Worf episodes, and it has one of the most chilling shots of Worf ever done. (the stepped zoomout next to the warp core) "The Arsenal of Freedom" is a really inventive episode, spotlighting everyone in a different way to their best. "Symbiosis" looks like a typical drug story, but actually has a bunch of really interesting twists about the Prime Directive and some intelligent scripting. (My favorite bit is when the aliens just blurt out that they have a plague to Picard, which means he must now quarantine the ship!) "Skin of Evil" is a much better episode than many people realize - it's full of smart dialogue and some really good performances. Yes, the alien is a walking oil slick - BUT look at the performances going on around him and listen to the description of what he is and how Picard beats him. I think that episode probably has Marina Sirtis' best performance in the entire series. "We'll Always Have Paris" is another one that's more than meets the eye - complete with some wild concepts and the fun of trying to transport someone into a "locked" room. "Conspiracy" is a dark and effective episode - it's never answered by any other story in the series, but it's frankly a lot of fun to watch. I'll admit that the final episode, "The Neutral Zone" is not so effective overall - but it does set up the Borg mystery and it gives us our first look at the Romulans with a spotlit entrance. Sadly, their dialogue is just awful - but the first sight of that ship is breathtaking.
If TNG could have maintained the run they were on into the 2nd season, the series might have taken on a completely different shape. But the WGA Strike of 1988 pretty much doomed that idea, and the delayed 2nd season limped through many of its episodes.
My point with all this is that if you look at the first season, you'll find around 8-10 really good episodes in there, mostly in the final batch of the year. And there's a strong sense of untapped potential with the show - that literally anything could happen. If you look at the final season, there's very few even passable episodes, and there's a strong sense of fatigue enveloping the whole thing. So if I had to pick between the two, I'd have to go with the first season.
DS9 is a very different story. That was a show that spent years trying to figure out what it wanted to be, and I tend to see it as a tandem idea with Babylon 5. Regardless of who came up with which idea, they were both major science fiction series set on space stations that were trying to grapple with both character stories and high concepts on a weekly basis. (When it came to casting, production value and basic scripting, DS9 was easily the one to watch. But I have to admit that B5 did have a fairly well-thought-out larger mythology, and a stronger overall arc. Sadly, B5 also had low production values, weak scripting and weaker performances much of the time.) My issue with DS9 for at least their first few years was that they seemed to re-think their series concept every season. The first season they were just trying to work out what they were doing. The second season got into a lot of Bajoran politics and spent time to set up the threat of something called "The Dominion". (And the Dominion was supposed to be an endlessly unravelling mystery, where you'd peel off a layer and see that there were ten more layers beneath it...) The third season, where Ron Moore came aboard, immediately dropped the complex Dominion concept and went with something much simpler. The fourth season gave us the sudden Klingon War. The fifth season abruptly dropped the Klingon War and went back to the Dominion. Frankly, after a while it gets dizzying. But I would agree that in the final seasons, DS9 settled into a consistent mode - essentially being about the Dominion War, for better or for worse. And the final batch of episodes put together for the series were probably some of their strongest. So I'd agree that DS9 finished much stronger than TNG - it probably finished stronger than any other Trek series other than Enterprise.
I have a feeling we haven't seen the last of DS9 in high definition, but it will be some time before anything further happens. I agree that CBS will want to have HD assets of DS9 and Voyager, but it's really a question of how much budget they want to put into that idea. Do they go whole hog as they did with TNG? Or do they just upscale what they already have? My hope is that we'll be given a much stronger indication about this when the final season of TNG on Blu is announced and released this year.