I've used the "warp points located anywhere in system" option exclusively; I think it makes the game a little less predictable, since you can have warp points right next to your homeworld. Or, even more interesting, within 2 spaces of the center of a black hole (THAT can ruin your day
).
As for "not all warp points connected", well, as you mentioned, the AI could have trouble with that. Maybe if you start with high tech, so they don't have to research Stellar Manip, it wouldn't be too bad.