The hatred for save points is well-documented: if you have been gaming for an hour and can't get to a savepoint and then get killed, that's pretty frustrating. FF XIII seems to have solved it by giving you savepoints pretty much every five minutes, but that's a bit grating too.
On the other hand, if you simply save at every savepoint, you know that you will have saved just before running into a boss battle. What if there weren't any clues and you cut through the monsters in an area like a hot knife through butter -- and then run into a boss that kills you? That would be frustrating too.
Last night, we played Eternal Sonata again. We saved and then went up to Mt. Rock. Everything went pretty well, but we didn't find a savepoint for more than an hour. We levelled our party up like crazy, though. And then, due to a lucky hit by the monsters, the whole party got wiped out and it was 'game over'... Gah.
Perhaps a mixed system, where you can 'save-at-will' and there are hints where you want to save, would work best.