Are there any important skills I am missing?
As the super-obsessed guy who wrote 50% more posts on this thread than the actual QM (spoiler: probably won't be doing that anymore since life is much busier now), I'm going to say right now that, while I probably
will look at this spreadsheet at some point, I can't see like 90%+ of the people who will want to read this thread
ever looking at it, much less reading the whole thing, much less than
that studying it enough to write effective plans that use it.
Probably the cardinal rule in making a Quest that will get a lot of active, informed participation is to make a simple, flexible system that inspires people to look creatively at the rules. A lot of the charm of the current research and Quarterly Action Plan systems was that so much of it was player-generated due to its open-endedness and flexibility.
@Yog's the one who came up with TIR shielding, the thermal annihilator and I'm pretty sure the variable wavelength laser tech;
@UberJJK came up with the finances spreadsheet and the ship calculator; I came up with the modular tech that's proven so useful so far. All of that was very engaging when it was created, even if it has since become complex enough to be opaque to new people, so the key to any revamp to the system will be to preserve as much of the openness and flexibility as possible while simplifying what we can to make it easier for newbies to absorb and master quickly.
Any system that
starts with 160+ skills is absolutely not going to be simple nor flexible, and I say this as someone who is a big fan of the quest that
@UberJJK still has in his sig as "The only quest where the Omake's are hard math." All you're doing is moving from one horribly complex system to another, and this time without the mastery that many of us oldsters had with the previous system. It's just not going to work: players just don't have the time to spend tens of hours pouring over a game system the way the QM will, since for them this will be simply one of many Quests that they will participate in, and you will quickly find your playerbase drying up.