This is my personal opinion and it could be right or not. If I were you, and I contributed to the article during the two positions (as a student and also as assistant professor in the new University), then I must put the affiliations of both Universities. Regardless of any other benefits.
Did you conduct additional experiment in your new university? Than you have to add your new affilation. If your revisions only in therms of comments and calculations in main text body, may be it is better to give first address that experiments performed. But in my opinion, adding new affilation is still okey in this case. I would like to wait others comments, this is interesting question.
I think, in an ethical point of view, it is better to keep your first institution where you conducted at least the main part of your research. You can probably add your new institution as your new affiliation and insert your present address.
I would write "On leave from First Institutute" and add an asterix with a foot note "present address is "Second Institute". Then noone will be hurt and you are diplomatic. I have been in the same situation.
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