I have a couple of different thoughts on mining, so I'll tackle them one by one.
Firstly, I agree with the sentiment that the high amount of miner incapacitations is more down to a lack of training, lag or sheer stupidity, than any kind of bad calls or skill failures on the player's part. Once you've done your first shift as a miner without falling down a hole, it's unlikely that you'll be seriously threatened out in EVA ever again. Therefore, I definitely support the idea of space mobs, both hostile, neutral and tameable.
I also like the idea of dungeons and treasures, though a design direction must be staked out whether these are for the miners, and yield unique equipment and mineral caches, or should be used to facilitate cooperation with Science by yielding artefacts and anomalies for study. The latter could distract miners from mining, and make them even more of a bottleneck.
While we're addressing mining, I think it's also high time for a meta-break. The kinetic accelerator with the AoE upgrade is the be all and end all of mining. Ripleys are too slow to be valuable, Thermal drills are too slow, and diamond drills only handle single tiles. I think it's time for a rebalance, where miner's equipment is balanced between three factors: Mining effectiveness, lethality, and treasure destruction. To counterbalance the fact that tools like plasma cutters might be really good in combat, miner armor should be less durable against tasers and bullets, and offer no protection from flashes.