If you want something totally awesome, question everything.
Almost every plugin I've seen continues on with the rather drivelly cargo missions (Exception: Angels of Vengeance for EV). What about getting rid of the standard ones and having a totally new set that fit your plugin. This, more than anything else, will set the scene and give players the feeling they are playing something new. It also means that they won't 'play it safe' by building up zillions of credits on cargo missions before tackling the proper missions -- they won't know what 'safe' is.
Question all the outfits and ships as well. A great plugin to look at is TOPS Mods (EV and EVO). Where is The Old Professor, anyway? TOPS mods alters a lot of outfits and ships. Without changing the graphics, it rewrites the text and the capabilities, and so, without a lot of rendering, you're playing a totally new game (easily the fastest way to get the new game feel).
Another thing to question is the 'we have to have pirates, renegades and aliens' cliche. We've all lived with this from the early days of EV. This may be cool if it really fits the story, but most great science-fiction doesn't feature pirates, and a lot of great SF doesn't feature alien races either.
If you're going to be rendering ships, go for a look that no-one has yet. Zarquon was working on some amazing renderings which looked like something out of Alien. I don't think he ever made them into a plug-in though.
It's also kind of cool to have a 'feel', and maybe some characters, running right the way through the text. Classic plugs like Clavius, Angels of Vengeance, Oreste and Eye of Orion do this. It makes for a much better playing experience.
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M A R T I N T U R N E R