Well this is an interesting thread.
I have very few hours behind EM cockpit, but I think I WILL post a reply here for two reasons:
a) I do have experience in other "space odyssey" (as I like to call the genre) games.
b) I think will be interesting to see the virgin/newbie look of an outsider on things (before the game itself "biases" my opinion).
...I might revisit this topic if/when I am more experienced to see if some suggestions I made are stupid.
So (and after reading other replies)...
1. I haven't played MP at all. I am still curious how people actually are in MP and each one also follows his own (SAME) quest line. Feels a bit weird thinking about it. I would expect MP to "open" either after the quest line is finished or in a pure "sandbox" mode (i.e. no quest line). I would expect MP to be mostly useful for MP-only (read: server only) tasks/missions or complete plots (drop in/drop out). And/or dogfighting between fractions. Esp. in "MP only" mode, interesting things can happen like specific players having specific tasks that completing them will allow the rest of the team progress (like "you get in that cave, kill some bad guys for us and reach for the main gate controls to let the rest of us in" or something).
2. I think the best save game policy is to be (a) when the user wants (what happens if I am in the middle of something complex but HAVE to leave? Pause and and keep it open for days?) i.e. Real Life to always take precedence. AND (b) in various key points (before and/or after a major mission, when visiting a station, before some serious decision). But keep a number of those auto-saves (NOT JUST ONE as this can lead to deadlocks) - maybe last ten (talking about auto-saves not manual saves).
Also two "badges" would be nice (so not enforce people): (a) a "play as we wanted" badge or something (for players NOT using manual saves but only auto saves) and (b) a "dead is dead" badge (that is initially given after the first mission and then removed from all saves on first dead). (yes keeping backups could exploit this but, who can fight that?)
3. Equal mix all the way. I suspect the game needs more variety. How do I know with so little play? BECAUSE ALL SPACE GAMES, ALWAYS, NEED MORE VARIETY.
4. Hmmm... Crafting system MUST ALWAYS be in, but needs some changes. Rare artifacts/components/ingredients. Some research. Parts from other ships (derelict?). Also I have to note something weird. I like the 3D craft GUI, but some things are conceptually weird. How realistic is to resize (in all three dimensions) the engine, without any specs really changing? Or, shouldn't adding short winds affect negatively the maneuverability of a ship in atmosphere? This part needs depth.
Needs more time? Take it. E:M is fantastic already, don't RUSH anything. I am all in for things that WORK, not are half baked (and not branded as half baked). Yes. X:Rebirth effect here. * Whatever you do in future development, always let your fan base in. But you already know that. Help them support you. Give them alphas, betas, more threads like this as things form. Better prices (I am Greek, I had to say that, it's tough to afford anything nowadays).
5. The more options the merrier. Jump drives. YES! Jump gates. YES! Anomalies/wormholes? YES! High speed drives? YES! (but only for shorter distances and NOT EVEN CLOSE as X:Rebirth implemented them) Malfunction for each of the above? YES!
Also whatever requires the ship's own "powers", make them really depend on this. So ability to do jumps, ability to do jumps-after-jumps (i.e. how many before cool down), jump distances (some should barely reach from edge of one sector to edge of next), cool down period (so how much time you are exposed between jumps) should all be proportional to the ship capabilities (and each ship have unique specs for them).
6. I don't even know what those do, but I expect them to be some large scale lethal weapons. I have general comment on that. I believe that "weapons of mass destruction" should definitely be in the game (up to the level of destroying a moon maybe, or a city) BUT except that they should definitely need to be ULTRA ULTRA difficult to obtain (missions, money etc.) they should also be having major effect on the player (a part that is universally neglected in implementing those). Something that will make a player that HAS one major weapon think twice (or three times or more

) before using it. Not "yeah I have a star destroyer thing but I now need to get away from those pirates so, let's throw this behind me and I will eventually buy another". NO WAY. Something to affect reputation, trade etc. Something major.
7. Haven't done much combat yet, but a general comment is to try and steal as much as possible from Freespace 2 (OSP) combat.

Definitely energy weapons should always balance with the energy capability (or set energy dedicated) of the ship, while other weapons (like missiles) not.
8. Hmmmm... tough question. I am always fore more realism. Yet what this game needs is more content. So I would maybe expect some growth in the planets but still far from "real" sizes (maybe just make them 10 times larger), but also way way way larger cities, more cities, more varied environments and more things to do (surfaces to make sense - and even subsurface and subsea where applicable). Maybe here the way to go (to keep sizes manageable) would be procedural/pseudo-random-generated construction (like Elite et al). What planets need definitely, is more life.
9. Answered above.
10. Well those I've seen are not very realistic. It really shows you just added them because you wanted to have them. If they stay (I vote yes), they need to be more realistic and have real usefulness (see again #1 for cooperative play)... maybe to board ships (so, space walkers), visit stations, go places not possible otherwise etc. I have to say, difficult for a single dev project.
11. I say yes MAYBE, but similar to #6. Someone having such a ship should be task-oriented and/or have real counter-effect on other things - and also be ultra difficult to have it AND maintain it. Also a big discussion if it should be remotely commanded, or take over a ship station (like a turret) or what.
12. Not sure how it works now, but I vote for having special things that are very rare (also useful to complete some missions or for crafting). Not sure if there is MP trading between players. If now, there should be.
Ah something else for the future. Landing on planets shouldn't be a given. Should need licensing from authority and ship (or add on) able to cope with atmosphere entry etc.
Maybe even varied depending on different atmospheres.