First of all, let me say I think the \'nether\' based warp idea is excellent.
What I was thinking is perhaps a combo of most of the above points. So a \'nether\' based area would exist. Let us call that hyperspace. In order to enter hyperspacae you must enter through a warp gate at a minimum speed. To slow and you\'ll just pass harmlessly through, although the gate will be drained / closed(See later).
Warp gates themselves can be found randomly throughout the galaxy as well as player made and act ONLY as entry points to hyperspace. They require significant power, dependent upon the mass of the ship that is passing through. Further to these gates, on ships larger enough to accommodate the bulk and power use, a kind of gate \'canon\' can be installed. This device would, when fired, create a gate x meters in front of the players ship which they may accelerate into to enter hyperspace. When fired these gates take all of the ships power and store it. At this point they act like a gate (with perhaps a timer before they expire to stop the server being littered by user \'fired\' gates. If the gate holds enough energy to send the ship into hyperspace it will, subtracting that energy from its total. If not all the energy will be used and the ship will pass through, closing the gate. This method will force players to think a lot about their power regen and thrust to ensure they reach a high enough velocity to enter hyperspace when passing through the gate. Secondly if players do not wish to be pursued then they will have to make sure they build a system which fires a gate holding the correct energy to correspond to their ships mass, otherwise the gate will remain open behind them.
This would also allow players to aid others by opening gates for smaller ally ships.
In hyperspace
Each ship would need a hyperspace propulsion system. The better the system the faster they would travel through hyperspace, in much the same way propulsion works now. Not good enough and you \'fall out\'. In much the same way as proposed before that so much distance in hyperspace corresponds to X times it in \'real\' space.
Navigating
I think you should manually navigate through hyperspace. Exiting it by slowing your ship below a threshold spawns you in the corresponding sector. This skill based system would also end up with over shoots, under shoots and \"accidently letting go of the \'w\' key\" - shoots :p and could lead to people exiting hyperspace in an unknown sector with no gate in sight. This would of course require some method of telling your relative position, but details :p
To stop \'warp by\'s (the process of entering an enemy sector, starting a fight, and running away), shields could be disabled once you enter hyperspace (no regen). Thus if you choose to flee from a battle by entering hyperspace, and the enemy pursues you, they\'ve got an even higher chance of finishing you off. Not to mention when you exit hyperspace you then have to wait for your shields to recharge, and perhaps your usual propulsion to re-ignite?
might not make much sense now its typed out, but in my head it does :p