For checkpoints, you can probably use one-way shield doors. Like, put a crate right in front of the shield door so that you can't get stuck walking into it, and you can't get into an area. To unlock the checkpoint, you have to use a min/max grav lift switch or something like that, which moves the crate and lets you through by coming in through the ceiling or something. Speaking of which, have we heard anything on Grav Lifts yet?
That wouldn't work. You would have to know about creating puzzle maps to understand the problem I was explaining; I'm not going to detail it here. Needless to say though it is an issue for us.