Actually, it is really a bit of slang. Calling something vanilla means saying it is rather plain, normal, or even boring. Hence, vanilla marines are simply an army that is created using the Marine Codex, without any variations/derrivations from the rules.
They are called Vanilla marines as it is a standard 'slang', not just for 40K but it many walks of life, it orriginates from ice cream, the normal flavour being vanilla, anything else you have to ask for specifically
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