This is also a point for package and connections skills.
If your engineer doesn't have all the specialties at one, fine. Add a level in a different specialty with a connection. Or have him take engineering from the package, and give it a different package.
And remember, Scotty would only be Engineering 5 each... after fourty years, and a dozen connections more than are allowed in MGT.
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Here's an option, tho', borrowed from LUG-Trek. Or, at least, how LUG-Trek worked with the people I talked with...
You take the skill in one specialization. Later receipts add either +1 level OR add another specialization, but at full level.
EG: Monty has Engineering (Jump Drives) 1. He gets a level of Engineering, and takes Enginerring (JD) 2.
Following term, He gets another level, and needs MD's, so he is now Engineering (JD, MD) 2.
Next term he rolls Engineering again, and choses to improve... to Engineer (JD, MD) 3.
He then gets a another a term later, and decides to add PP... Engr (JD, MD, PP) 3.
This could be applied to any of the skills with specializations for a more space-opera feel.
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Option 2: The TNE way ....
Simpler, far more epic...
You only ever get ONE specialization... but you have the rest at half level, rounded down, rather than just at 0.
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Have fun!