Zenfur This was a significant difficulty, how to craft a campaign with the very limited form that exists at the moment, tiny briefing texts, no in-mission dialog and a branching mission path. However, Duskers manages quite well to deliver a story based on similar constraints, and I
shamelessly stole took much inspiration from it. The main trick is to have the en creux player character being the only person left, and have the entire story delivered as short monologues/comments/journal entries in each situation, trying to find out what happened (and also survive).
The biggest advantage is that it props player imagination to unpack it and fill the blanks
a lot, which is both economical and gets the player to imagine a better version than what could be done. In this, it is rather similar to flash-fics. I think this should be enough to work, without requiring to remake it entirely or add much more difficult and/or expensive features like voice acting, player-driven interactions or even cutscenes. The format become more of a deliberate choice for the story, and avoids "feeling cheap" as could happen with a more ambitious presentation on a restricted budget.
I do fear that the open-ended payoff may not be satisfying enough: I cannot simply explain the mystery completely, as no explanation could measure to what the players imagined, but getting the right clues to let them reconstruct an interesting version of what happened is rather difficult. The story will probably need at least a few iterations before being release-worthy anyway.
As for the "looking cheap" problem in-game, the biggest offender for new players IMHO is the particle effects. Shaders have been around for a long time, and people are now accustomed to see SFX using them. Nanolathe, large explosions like nukes, or the Bertha muzzle effect, for example, feel like they're a decade old - even if they actually look quite nice for us. The nanolathe effect is even lagging due to particle speed, which is especially visible for long-distance caretaker tasks. Compare this to the pretty nice construction effect on the unit: despite being quite simple, it feels much more modern.
Replacing or completing those effects with shader effects would go a long way to make the first impression feel less dated.
The second one is probably the animation system, but that would require so much work rewriting the engine, I doubt this is an option.
A distant third would be to have some simple map border landscape. Supreme Commander 2 (of all things) seems to do that well, with the map landscape seamlessly continuing outside of the borders and making the map feel it is somewhere, instead of being a cut-off rectangle in the void. It may or may not be a good idea to bend the outside landscape as well, as Zero-K has the same unabashed toy-unit feel than Planetary Annihilation, implying that the maps may be as big as small continents. But this would be so much work, it is almost certainly not an option and we'll have to make do with the map-repeating plugin.