Could be they just saw no reason to bother because there was no possibility of getting him. There is no requirement to indict someone immediately upon collecting evidence, indictment is merely the formal accusation of a felony issued by a grand jury. I don't understand why some of you seem to consider this some wild thing. Furthermore, even if they had all this evidence nobody may have sat down and come up with a legal theory sufficiently tailored, and in fact you yourself raise this in the rest of your post:
>Obama DOJ had decided to not indict Assange for this, this is a politically motivated prosecution by the Trump administration.
Your source does not support this leap. In fact quite the contrary:
>Justice officials said they looked hard at Assange but realized that they have what they described as a “New York Times problem.” If the Justice Department indicted Assange, it would also have to prosecute the New York Times and other news organizations and writers who published classified material, including The Washington Post and Britain’s Guardian newspaper.
Your quote doesn't even make sense exactly because prosecutors never "have to prosecute" anything. But that aside, what we see now is that they haven't indicted him for "publishing classified material" or anything like that, they've found a genuine potential crime (if proven) that is about direct material aid provided by Assange alone. Going after publishing would invite all sorts of 1A arguments and would probably fail unless the papers were directly involved. But unless the NYT and others were in direct contact with Manning and trying to help her break through government security themselves, this charge doesn't in any way involve them.
I mean, you do see how your own accusations here are symmetric right? Someone could just as well argue that it was Obama making a politically motivated decision not to indict, though I think that'd be a silly argument too. Ask "if at some point in the last 7 years Assange had suddenly voluntarily left and returned directly to the USA and announced he was willing to face whatever they would bring, would the US have then prosecuted or not?"