Well, by nature games "lock off" content for certain actions in how you have to beat a boss to move on with the game. Things just get more complicated. I mean, think of Mass Effect. I have never heard Kaiden's lines in ME2 or 3 because I saved Ashley. I haven't heard most of the romanctic options for the cast as that requires multiple playthroughs, both for different characters, but staying faithful or cheating. A lot of these things can be minor, but from the early days of rare drops in Final Fantasy 2 (4), little things got kept from us.
As for endings, it depends on how it's done. Chrono Trigger was less a denial of a true path than some "what if" scenarios really only gained through new game +, so that's not an issue. Persona 4 on the other hand is first and foremost set around a murder mystery, and the game gives you the worse ending for fingering the wrong culprit. It makes perfect sense to do so as this was the real challenge to the game, not beating shadows. Kill the innocent man, you lose. It's simple. It's annoying, as most of us really don't think that way, especially in a video game, but it is logical to pull this here.
To a certain extent, I like multiple endings like this for that reason: they reward positive actions. I save everyone by being smart or considerate, I get a better reward that the guy that leaves someone to die. I do everything the game offers, I get a better ending that the guy that only did 60% of the content (and laugh at the irony that someone might complain about being locked out of a part of a game because they chose no to partake in another.) This isn't to say it's always done right. Chrono Cross' true ending was fairly ambiguous to get, and Disgaea's is sabotaged by encouraging things that rack up ally kills. On the other hand, things like 9 hours, 9 persons, nine doors, and Virtue's last reward were unique in that bad endings were required to actually get the good one, so there can be some uniqueness to it. Even without that, it's part of what makes a true ending fulfilling. Seeing the outcome of killing Richter Belmont in symphony of the Night, makes you feel more fulfilled when you figure out how to save him.