OK, there is a lot to comment on this thread, so I'll try to be organized...
Final death: Since your save doesn't get erased on full death, I find that the situation where you are not-quite-dead are a bigger penalty as they come with a permanent injury. I would suggest fully removing final death, but instead making permanent injuries more common, or maybe add semi-permanent injuries which can be healed by doctors, but at a very high cost (around 100'000 or so). Heroism could help you avoid permanent injuries ("just a flesh wound"). Oh, and cyberware should have a chance of being damage (needing replacement) when you "die" in personal mode, in a similar fashion to getting your mecha junked.
Also, in my previous and current games, the only time I ever reloaded from a save was when my initial lancemate died (or when I died myself). I would have to say that this is the only situation which you cannot come back from. Mercenaries and others are fair game, but the first lancemate have more of an impact. I would extend the contractual immortality to them, but then some new balancing mechanism would have to be added as they cannot use cyberware.
Science: Science, beside robots, is a purely content-dependent skill. It's usefulness is directly linked to how much content it gets. A way to make it more useful would be to add new loot that can only be obtain using the Science skill on dead robots. That loot should be good enough at all points in the game to be worth a skill, and should not be overshadowed by items you can readily buy. This link to the invention system, as the loot could simply be made the ingredient for it. An idea I had would be to have items like "Ultra-light alloy", "superconductor coil", "micro fission core", which could be permanently attached to mecha parts to improve them, a little like add-ons, of course with a limit of one per part.
Survival: Survival is pretty much the equivalent of Science, but for natural creatures instead of robots. I have only ever used in GH1, but from what I could see from the content files, it still isn't a worthwhile skill. You get what? A good shield, a good grenade, good foods, some cash and some XP. The XP can easily be bought from a trainer, and you would get more cash by taking up shopping instead. I'd prefer to see Survival gets more single use loot, preferably for effects that are not achievable otherwise. Examples could be food which restore SP or MP, glands which refill your batteries and fluid which give some kind of one time buff.
Mysticism: Mysticism is the exact same boat as Science and Survival. One idea I had to make Mysticism unique would be to play with the relation it seems to have with artifacts. Many artifacts in the GH universe seem to be understandable only through Mysticism, examples being the crystal skull. So why not require Mysticism to unlock the full potential of the artifacts? Each artifact could get an upgraded version which could only be reached with a successful (hard) Mysticism roll, with a limit of one roll a day.
Another idea I had about Mysticism come from its interpretation as being the specialty of meditative monks. Mysticism could give you access to mantras, which when activated (only one active at a time) would give you some bonus, but drains your MP. The active mantra could get turn off only after a given delay, or when MP reaches zero. Then either the Mysticism skill could be used to unlock more powerful mantras, or would slow down the MP drain.
Some mantras ideas I had, together with the requirement to be able to use them:
Concentration (requires Spiritual > 0) Repair +1, Medicine +1, Speed -5.
Bloodlust (requires Passionate > 20, Mysticism > 5) Mecha Fighting +2, Close Combat +4, Mecha Piloting -2, Dodge -4.
Fist of Steel (requires Close Combat > 5, Mysticism > 5) Fist DC +5.
One with the Universe (requires Spiritual = 100, Mysticism > 10) All stats +5 (huge MP drain).
Rising Anger (requires the Badass talent) Drain morale.
Eagle sight (requires Mysticism > 5, Awareness > 5) Perception +5.
Rabbit motto (requires Wangta > 0) Speed +10, All skills -5.
Just my suggestion for a "buff skill" Mysticism that isn't actually magic, but really impressive self-control.
EDIT: Science/Mysticism/Survival are also currently quiet useless for lancemates, as you can only use them (with the lancemate skill value) when in a safe spot. This is even true when controlling the lancemate in tactics mode. I would suggest that any "s" skills that lancemates AI doesn't use by itself (like Repair/Medicine) should be usable by the main character with the best lancemate skill value, and that
in all situations.