"Intra-system" and "Inter-system" ships are a good idea, but the way you suggest implementing it is slightly out of focus. The difference between these two types of ships is the ability to use warp-points. I don't think that ENGINES are involved in using warp points. What would work better, I think, is to change the use of warppoints to require a special "warp activator" component in the ship that allows it to pass through. Without it, the warp point is just empty space like any other sector. This component could be reasonably large to make it relatively costly in supplies/weapons capacity for a ship to have warp-point capability. This would also explain why fighters cannot warp. They are too small to carry the component (the tech would have a 'minimum' size).
This does immediately bring up the idea of ships which can carry/tow other ships through warp points.
Maybe you could let a fleet with at least ONE warp-activator pass through a warp point, leaving the interesting possibility of ships getting stranded if their "warp helpers" get bLasted. Or maybe we could have some sort of genuine towing rig added to the components in the game. I'd like to see this regardless of whether the use of warp points is changed.
The next step in excitement is controllable warp points - i.e. "Jump Gates"! I hope those get implemented for the final release. Properly used, they would let you accomplish many things with smaller numbers of ships than you would otherwise need.