I think that if you have a fleet (this isn't for fighters), you should be able to switch inbetween control of different ships. Maybe that's a stupid idea, you would switch veiws a lot then. but they could make it so that you can have window showing what that other ship in your fleet is doing and if you decide to switch ships it is instant and the windows switch and you're orignal ship is in a small window and your current ship is in the large window. That could be a feature you turn on and off, or it could only come on when you are under attack.
Another thing is, I want to have more options when talking to other ships. There could be different things depending on the situation. Things like "Do you want to Beg for Mercy", "Thank-you" (I'm a polite kind of person and i feel bad when someone halps me out, and i can't say anything to them) , "Can you help me with this mission?" (they could give you a hint or say no way. You could choose what mission you want help with), "I help you" (for battles, when you are trying to get on one government/race's good side, you could use that and they would know that you aren't shooting at them, and it would earn you good credit with them), there are a lot more talking things that there could be, but I'm going to move on.
Why is it that you seem to be the only one who affects the universe's fate? Sometimes planets/systems/boarders should change sides. Stuff about the battles should be in the news.
If you go to an uninhabited planet there should be options, like: "Explore", "Scan", "Is there anyone else here" (there's probably a more concise way to put that.). All of those options could be used in missions, there could be a mysterious map (sound corny, i know) and you might have to take it back to the government who sent you out, but you could look at it first and study it. You may even decide not to take back to the government, but to keep it for yourself, or make a copy of it. The scan option could be used for finding ruins (as part of a mission) and "Is there anyone else here" could be used for bounty hunting type missions, I mean, really, if I was being chased I wouldn't hang out on my ship all the time, sleeping on the ground, where no one will suspect seems like a better idea.
Back to the map thing. If you find the "mysterious map" maybe it could show an area of the universe that you can't get into, or someones hidout. I dunno, but there are a lot of possibilities.
I think that EV3 needs cool plots that change things and are more realistic.
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