1. I'll jump on the engine made for everybody bandwagon. Too many of the features of the EV3 engine are broken or don't work as expected because Nova never used them.
2. Greatly greatly increase the numbers of every resource. 1000 missions, 256 weapons, ect are all too low. They need to go way way up. It should be at least 10x more than the EV4 scenario requires. Because who knows, someday something even bigger might come along.
3. Get away from the old resource fork format. Instead of distributing 33+ 16MBish files we could ship 1 300MB+ file. This would also make it much easier to use large ship sprites and stuff since you wouldn't have to keep the ship sprites below the ~16MB limit.
4. How about more interesting cloaking options? Different types of cloaks that can be seen by different types of outfits. Think of something similar to the 4 missile jamming types.
5. Take the key carried concept further so it can actually affect ship performance, weapons, everything. Sure this can be faked to an extent, but its not pretty.
6. Draw to the screen correctly. This would get rid of the bleed through and Exposé issues.
7. Millions of colors.
8. Better beam and other per frame stuff handling.
9. A better BBS system. Take it beyond a fairly boring single list of missions. Make it multifunction, more dynamic and so on.
10. Big planet scaling in com dialogs
11. Better handling of multiple objects of the same type. For example just have a single Hypergate spob, and allow it to be named different things in each system its in, instead of needing dozens and dozens of spobs. Want to change a stat of the hypergates now? Have fun doing it many many times. Ares did this and it was much better.
12. More ship animations options and more control over them.
13. Definitely more in flight scripting options. It was amazing what you could do with Ares and its limited scripting, a real scripting solution would be amazingly powerful.
14. Ares style zooming, and in system FTL engines. EV feels squished together where Ares had huge distance between planets to fight in but it didn't hinder getting from place to place.
15. More and better AI options. Perhaps a simple AI scripting language that can be used to vary a ship's behavior based on situation more than "standoff attacks"
16. Smarter dynamic mission destination choosing. Stop eliminating the important planets from random mission destinations. Surely there is another way to prevent bad destinations.