Simple Effective Progression
The two types of progression I'd like to see:
Rather than limiting what blocks people can make, limit the quality of them based on skill. I imagine a skill of 1-100+, every time you build or repair (# of blocks = level * some constant), the skill goes up. The skill would give a passive bonus, like a thruster skill would make thrusters you build or repair have a % thrust bonus equal to your skill level. It's simple and allows for specialists in multiplayer to enhance team work.
More ores/ same components
They could add more ores that make the same types of components, but they could have small passive bonuses. Titanium as an alternate to steel plates for hulls,maybe Germanium as and alternative to silicon for computer components, Neodymium for motors, etc. The integrity of blocks is already determined by the sum integrity of the components. Maybe thrusters and reactors could have their outputs be determined by the sum of their components' quality. Medieval Engineers already does allow for alternate materials for some building and cooking recipes, though I don't think there are stat differences based on such.
These seem the best to preserve the feel of SE because they wouldn't hinder creativity like block limitations, they would give a potential for a subtle uniqueness to each play through, and it would add enough complexity to prevent a sense of monotony in your mining goals.