I can accept a certain amount of change in video game franchises, but when you take away the basics that made the game unique just to fit in with the current standard, that's when I have a problem. I'll go ahead and request anyone to play the very first Final Fantasy game on Nintendo, then play the latest version. Skip all the stuff in the middle, and go by those two games within the same franchise. You'll see some similarities from the original in the newest version, but they are so distant on all other aspects as to nearly make them completely different games, just joined by a similar title.
I agree that Fallout has fallen quite a bit from the first two in the series. I don't think every single game needs to be modernized when there was nothing wrong with it in the first place. Slapping a new GUI or graphics engine doesn't really constitute a great sequel. GTA is one of the few games I can think of that actually benefited from that change and helped to make the game more deep for the player. Fallout didn't need a to become a FPS in order to survive for me. The third-person isometric view was fine for me, and I'd have been happy to see it continue along that path, maybe with the option of being able to turn the camera. People crapped on Fallout Tactics, but they did little to change the game itself. You were dropped in an area, given the same format as the previous two games, but now you had to consider the factor of line-of-sight when attacking an enemy. There was still a story, maybe not the one you were totally familiar with since it took the angle of the Brotherhood of Steel. I played the hell out of Fallout Tactics, and even enjoyed the multiplayer on occasion (when my brother didn't mind getting his ass handed to him with a Neostead from a robot when he tried to rush my team in a house). It was a slightly different flavor of a franchise we'd known and were familiar with.
How about the Harvest Moon franchise? The basic game mechanic hasn't changed over the years. You still farm, try to balance a social life and make money. Some of the faces and scenery have changed, but the fundamentals are all still the same. When they attempt to add gimmicks to change the game from the original formula, I think that's where people tune out. You need to add a few subtle changes in order to stay somewhat with the times, but keep it within the right context. I didn't really want to talk about CoD, but it's pretty hard not to within this topic. I haven't seen a lot of innovations in the last three games. They change a few weapons around, but that's basically it. Maybe a minor graphical tweak here and there, but they are still pumping out the same generic shooter they've always put out, and it is just getting stagnant.
Saint's Row has done a good job in the last two games of keeping the story straight and remaining faithful to what kept people coming back to play the game without getting annoying about it. Adding more speech to the main character was a nice touch over the first game (where you only spoke two lines in the whole game), and they took out the bonus you got from having to color all your cars purple to impress the gang (I did get a little tired of that color after a while). The city didn't change so drastically that you couldn't tell it apart from the first game, they changed the names of the gangs around to reflect the progress you made in the first game, and just stuck with the same familiar game and changed little things here and there to make it stand out just enough as a new game without having to reinvent the entire franchise. More companies need to pay attention to this example and do what they can to follow suit if they want to keep up the popularity of their franchises.