Yeah, there's a lot of things the game could be improved with. A lot of them are either already known and planned for by developers, or theoretically possible already with mods.
I'd like to see naval units and aliens (and resources, and having to dispose of dirty water adding water pollution and invoking the wrath of amphibious aliens), flying aliens, more defense and offense options (RTS elements akin to a cross between Majesty and Total Annihilation), and some more in-depth crafting and research trees. More power options, survival elements, suchlike.
I had a neat idea (after seeing the loader in the devblog, which I have to say would be unbalancing to the game unless limited) for "Assembly Line" buildings. Three by three like Assemblers, they'd be a cross between an Assembler and a chemical plant. Basic Assembly Line would be researched at about the same point as Assembler 3, and take some fairly high-tech resources to make (smart inserters, fast belts, processor chips, speed modules, maybe lubricant). It would, in effect, be an Assembler with a ludicrous base production speed, like 2.5. Two caveats - it can only produce things that take 1 resource, and can't be loaded via Inserters. Main feature - it has one "input line" and one "exit line", like an inline chemical plant on a conveyor belt instead of a pipe. It will take its target resource off the input line as fast as it will come. More advanced assembly lines (in addition to being even faster and more difficult to make) can take two or three input lines, but no more than that, and they will all have you do the "match the input line" minigame that chemical plants have with multiple inputs. For making the big, complex things you'd still use Assembler 2s and 3s, but for various cogs, cables, and electronic boards, you will eventually (since it will be pretty late in the research) want to simplify and speed up the production process, which I think these Assembly Lines could achieve without being unbalanced.
More than some other things though, I'd like to see some lore and appropriate complexity added to the game. I mean, the setup you have at the start of freeplay doesn't quite make sense unless you put thought into it. You are supposedly an engineering specialist with some pretty advanced tools at your disposal, you can build some pretty neat things from the get-go but you have to research some fairly basic processes like steel processing and wall building. I'd like it to say somewhere that, for example, you are an engineer
in the future, so a lot of the more basic processes you simply are not expected to deal with - and knowing how steel is processed does not equate to knowing how to build a steel smelter out of what you have on hand.
For instance, research. I'd like research flavored into being an automated experimentation process constructed out of simple electronics logic. Instead of preset research packs, you could be feeding the labs with resources and processed items relevant to the research, that are used up in the experimentation. It makes more sense than "research packs", and detrivializes research, requiring you to either shift gears as you switch projects, or choose your research queue such that you don't have to.
Power, too. For some reason you have to start out with giant steam engines for power, when it would make sense to start with smaller things - like burner generators. Steam engines are great for supplying huge amounts of power to a large factory, but to start out you could use electricity generated by small, coal- or wood-burning 1x2 powerplants. You could make burner inserters more difficult to construct then (and properly relegate them to "backup" tier), and maybe even make conveyor belts require power, with the caveat that belts carry power for themselves as long as any belt in a connected line receives power. You could properly have offshore pumps require power as well. A lot of "common sense" problems with how the game has you start out could be solved by your character, being an engineer from the future, knowing a simple and efficient way of extracting electricity out of heat. (some variant of a stirling engine?)
I'd start making a mod to that effect, but my creative drive has run out.