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Fully trained technician has better shield recharge/repair bonus and better accurancy but need tons of exp.
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I forgot to mention, but this is not correct at all... The Systems Software MK3 has Technomage, Expert countermeasures, expert shield operator, expert repairman, so the repair/shield bonuses are exactly the same as an expert technician, minus the engine improvements (which was given to the Piloting Software instead). The only bad thing about MS pilots is that they are overspecialized, that same systems operator only has Piloting 2 and Weapons 2.
Though, a technician may have higher survivability if he has any of the piloting survivability perks (Tactician, Hard To Kill) on top of his technical bonuses. But you would require practically a maxed out Technician in order to surpass that, while you can get the Systems Software MK3 very early in the game.