I could have gone through the hundreds of games and just picked the top 20 that had the most influence, but even that would be a faulty list since there would be a temptation to only add the popular ones. Dark Heart of Uukrul has a lot of great ideas going for it, but it was a commercial failure. Should that game be on a top 20 list of games developers should look at or not?
You answered your own question earlier. This isn't a list of "popular ones". The point of such a list would be for designers to see unique features being implemented. You either pick the oldest game that implemented it because having to deal with technological limitations to do so teaches you a lot about how to implement features efficiently, or you pick whichever game implemented the feature best. So I'd pick either Rogue or Nethack because Rogue started it all, but Nethack took the complexity to incredibly high levels without losing the essence of what made Rogue Rogue, whereas I'd argue that games like ADOM or Moria did change that essence, by turning quick-playing perma-death games into extremely long excursions that still have perma-death - a very different kind of game when you think about it. Final Fantasy has no place there because it doesn't matter how successful it is - it didn't actually do anything that special or different, beyond codifying already existing mechanics.
I included Might and Magic 1, but the series departed sharply in style and interface with Might and Magic 3 and again with MM6. Shouldn't Might and Magic as an entire series be considered because of the innovations made each time
No, because the reason to include any of the games in the first place would be because they were the blobbers to put so much emphasis on outdoor exploration and a completely nonlinear main quest that you had to piece together bit by bit in its entirety. The only reason to include anything other than MM1 would be if one of the games improved on this aspect dramatically, and I don't think any does, regardless of the quality of the exploration.
The small innovations of the 11 Gold Box games are significant over time, and so they would be worthwhile to play the entire series through for the better graphics over time, and milestones like the first in-game romance.
This is a list of games ever designer should play, and supposedly learn from. "Better graphics over the time" does
not qualify. The romance in Savage Frontier might, except it's such a minor mechanic and so irrelevant to the game as a whole that I don't think it's justified. Frankly, much as I like the Gold Box games, I wouldn't include them at all. The only one I might include, if I have the space, is PoR, but more because of its extremely clever use of a low-key non-epic plot, the fact most of it takes place in the city streets (count how many games before it did this... or even after it. Legends of Valor, which was otherwise a terrible game. AR: The City, which had no real game in there to speak of. What else?), and its use of the overland map for exploration.
Finally, what about the bad CRPGs that still had something to offer?
A truly terrible game whose horrdiness can teach you what to avoid in your own design definitely has a place. I don't think DAO qualifies because it is merely mediocre and boring, not "WHAT THE HELL WERE THEY THINKING" bad. If anything Descent To Undermountain would be a great example of how to NOT use an engine that is TOTALLY INAPPROPRIATE for the kind of game you are making.
Anyway my own list, which mostly intersects with yours acually:
Rogue
Nethack
Oubliette (PLATO)/Wizardry
Dungeon Master/Chaos Strikes Back
Temple of Apshai
Ultima IV
Phantasie
Tactics Ogre
Wizard's Crown
Pool of Radiance (SSI)
Demon's Winter
Wilderness Campaign
Quest for Glory I
Wasteland
Daggerfall
Morrowind
Might and Magic 1
Planescape: Torment
Mask of the Betrayer
Dark Heart of Uukrul
I can justify every game on there as being the prototype of a very specific mechanic or concept, and in the case of concept it's one that pretty much defines the game, as opposed to being a minor feature. Tactics Ogre was hard to justify, but considering it pretty much started the "strategy RPG" genre I couldn't really leave it off. I almost didn't put Dark Heart of Uukrul in there by the way (I had Magic Candle initially), even though it's a better game and a better CRPG than half what's on the list. I simply felt that it's game that does everything right rather than a game that attempts something truly momentous and that one MUST learn from. That said, the fact it
does everything right is the reason I included it, and because I also remembered it probably shares the slot for most unusual ending with U4, for completely different reasons (it's the same reason I had Magic Candle in there initially).