'Soon will be a' is not as close to the intended meaning as 'soon becomes a'. Becomes means a change from one state to another. 'be a' doesn't have that meaning.
I would drop the comma before 'soon'. I like 'will be' more here. What seemed a natural choice will be a dream some time later in future. I would have used SP (becomes) here if I had spoken in general.
what seemed a natural choice is the subject. It is incorrect to separate the subject from the predicate with a comma. Secondly, seemed is past tense, and becomes is present. This is jarring to some, but not incorrect.
With no implication that these are the only correct phrasings, I would use these versions: