One of the biggest problems with Space Engineers in my opinion is a lack of objectives. There may be some implied objectives in the game like surviving and killing pirates, and the player may be able to come up with their own objectives like visiting every planet or building a huge ship, but that still leaves players wondering what to do next. Many worlds of mine have been abandoned because of this, plus there are so few objectives that accomplishing one is rare. Delayed gratification is a big part of games of this variety but in my opinion Space Engineers takes it too far.
I propose that Space Engineers needs missions. Perhaps they could be obtained from NPC bases, stations, and ships which would make the world feel more alive and give credits which can be exchanged for resources (or maybe just resources) that can make early game less tedious and add more ways to advance, it could even make use of the communications system for contacting stations and getting missions. There could be a variety of mission types like "assassinate this pirate", "transport this cargo to the Mars orbit station", "salvage this important thing", "destroy this enemy station", "preform stealthy reconnaissance", "protect this allied ship/station from pirates", or anything else you could think of. It could even have workshop support.
On top of this stations could have limited stocks of items that replenish over time and each station could have it's own prices for things making trade routes possible. Perhaps there could also be the ability to raid these NPC stations, it would have to be difficult but profitable. The stations could repair themselves again over time so they will come back online and the responsible player could take some kind of reputation hit. Having multiple factions that the player could align themselves with would make it all the more interesting.
This would also be a great way to introduce lore. A mostly uninhabited Earth-like world and an alien planet in the same star system is definitely suspicious, maybe it was terraformed and the space engineers are there to prepare the system for future colonists. Perhaps conflict between factions ended up causing problems on the colony project, keeping the system relatively lawless. That is my headcannon anyway, the possibilities are almost endless though.
Maybe all of this is a bit ambitious but in my opinion this is really needed. The biggest gameplay element in Space Engineers is part of the name, creating practical engineering solutions to problems in space. The only thing better than finishing an advanced and amazing ship is seeing it in action, and I can't think of a better way to do that than a mission system.