I see your point - in some ways , yes, it would be good if mining were a really excellent puzzle game. However, the MMO-nature makes game design very difficult - if you spliced SpaceChem into the mining system wholesale, you would annoy a lot of people who like the present system, please a few people like me for a short while - but then the SpaceChem levels would have well-known published solutions, or (if they were randomly generated) the puzzling would be automated - and we'd be back to the mining-by-time system.
(And I would loathe a system where you buy the game and then have to buy the level solutions list or bot in order to be an effective miner/industrialist/whatever.)
For example, Puzzle Pirates is an MMO where most of the verbs in the game are themselves fairly difficult-to-automate puzzle games - but they do have problems with bots.
As I understand it, MMOs and non-MMO games offer two different pleasant experiences, and neither substitutes for the other. SpaceChem has no pretensions of worldiness - there's no economy behind it, and you can't affect other players. Worldiness, economy design, making everything connected and relevant to each other, and durable, long-term play is what MMO game design is about, and what Perpetuum offers that SpaceChem cannot supply.
By the way, did you play it? Do you have any interesting solutions from the first four planets? (I don't want to spoil myself)