Not necessarily, and I think that Final Fantasy is a chief example of this. On a basic level, one could say that Final Fantasy 1-10 are pretty much the same. In a very basic sense, one would be right. However, when you start to look at each one and look just a little bit beneath the surface, one starts to realize how different each game is, and they only become more diverse from there.
Not every series needs to do that. Heck, I might say that Final Fantasy is something of a minor extreme in terms of making each game different and trying new concepts, so we take a look at Fire Emblem. Fire Emblem is a series that is identifiable by its gameplay, and when one plays a game, they'll know it's Fire Emblem because it feels like the others.
So why do I think this is a good example? Because it knows how to play it safe and still introduce new concepts. I could play Fire Emblem One and not feel too jetlagged, but it wouldn't feel as much like Fire Emblem. However, after they introduced the Weapon Wheel, they didn't stop there. They tried to make each game feel like its own game, introducing and removing mechanics so that no matter where one looked in the series they would see a unique experience.
Another example, and I think this is incredibly relevant, is Shin Megami Tensei. Shin Megami Tensei and Pokemon are pretty similar in many respects, but the difference between the titles is that Shin Megami Tensei didn't have to totally change it's genre or gametype to feel fresh but it still managed to evolve without feeling like it was stuck in time. It managed to apply that modern coat while adding more and more to the game, as if the game always had more to offer you, but it still felt like Shin Megami Tensei.
And those are just a few examples. Turn-Based RPGs of any kind do evolve and they do change. Some make drastic, series altering changes and others make traditional but still sequel worthy changes. Pokemon does add things, but at a much, much slower rate. Heck, I'd go as far as to say that XY should be the fourth generation game, because if you culminated all that was added between DPP, BW/2, and XY, you'd get enough content to warrant a sequel. On their own, however, they just don't add that much (well, except maybe XY, but that doesn't change the point. It doesn't have to be like Final Fantasy and play with other genres. and it doesn't need to completely rework its gameplay, but all I know is that over the past couple of generations, it's been doing what it can to get the most money the fastest possible way, and XY is my ray of hope that they are starting to care again (as was BW/2, but we'll see).
As for Red/Blue and GSC, I can go on record and say that I can't really say those problems are deal breakers for me or for most of the people that play/ed the games. Sure, they were hard compared to the current ones, but I think most people will agree in saying that the recent games aren't that hard. I think RBY/GSC had a moderate difficulty (though I hear BW2's doing a good job bringing it back). As for post-game content, that was fine as well. Sure, there were no battle frontiers or Sevii Isles, but that didn't stop people from getting tremendous playtimes and always finding more to do. As for the type diversity and the rosters, they weren't huge problems, and they certainly weren't problems that made you want to throw your system at the wall because the forgiving nature of the pokemon series always balanced that out. Plus, as you said, those were merely technical issues, and they're hardly deal breakers. They aren't minor, but they could be fixed easily. And they were. Heck, there are people that go back to play the games because of those things. That doesn't mean we should overlook them, but the music in the first two gens was so great, and they still did well at what they did, offering memorable characters, locations, and story that people never forgot. They didn't mind the technical "problems" because they had so much fun with the game, as well as with the technical problems, that they enjoyed the problems themselves. If we were to look at each title as if they all came out at the same time, maybe outlook would be different thanks to the different features, but regardless, people like the games, especially GSC, for their merit. People like RBY/GSC not just because they were something fresh, but because they complimented each other as prequels and sequels. They had a lot to offer, and a lot of new to offer. If BW had been the second game or if DP had been the second game, all with the improvements that the games that preceded them had, they would have been meet with incredible praise because as sequels to RBY they work. However, as sequels to RSE/DPP and RSE respectively, they just don't cut it as full blown sequels.
As for the games you listed, I don't think Zelda II is bad at all, and I think Gamnonbanned and AVGN highlight pretty well the reasons why. It was hard, I'll give it that, but it set in place RPG elements and a open world that was unseen in a NES game, and the music was still great. Sure, it wasn't LoZ, but I'd hardly call it bad or even anything but good.
Same with Adventures. I'm not going to say it was great, but I think people would have looked at the game rather differently had it gone with it's original concept and passed up the Star Fox coat. People can sometimes be averse to change, and I realize that there's more than one franchise out there that would have gotten a lot less flak if its "black sheep" title had different name.
Eh...sorry for the wall of text. I just started typing and realized that I had a lot to say, I might have went a little overboard, though -.-'