Just to rave a bit more, I also love how relentlessly clever VVVVVV is with its gimmick, throwing rooms at you that just have you doing cool gravity flipping stuff. The room "Just Pick Yourself Down" makes me smile every time.
There are some rage moments but the ridiculously friendly checkpointing makes it work, keeps the pace working very fast and makes up for whatever flaws would be much more visible if you were actually being asked to do these levels without dying.
Yeah, I was really expecting something jerky, like having to redo an entire level or respawn several screens back like in Mega Man. Instead, like you said, the checkpoints are quite logical in their placement (even one midway through an early auto-scroll section!). I'd also add that when you die you're treated to a very, very, very brief and non-dramatic death and zapped even more quickly back to the last checkpoint. It's a minor thing but it really takes much of the sting out of dying.