Mueller's investigation was never mainly about Trump. It was about Russian interference in 2016.
That may seem like a distinction without a difference, but let me explain.
Here is the original, short letter from Rosenstein regarding Mueller's appointment as Special Counsel.
https://www.nytimes.com/interactive/2017/05/17/us/politics/document-Robert-Mueller-Special-Counsel-Russia.html
Yes, "collusion" between Trump and Russia ("any links and/or coordination between the Russian government and individuals associated with the campaign of Donald Trump" ) was obviously a part of Mueller's very broad mandate, but it wasn't the only part.
This is not to get into all of the myriad manipulations, interference, witness-tampering, intimidation, LYING, destruction of evidence and paper trails, and other corrosive behavior on the investigation from Trump and his supporters foreign and domestic, along with the steep burden of proof needed for these crimes.
Remember: Robert Mueller is an old-fashioned, small-c conservative (and Republican, incidentally - not that that matters now) man of the law: a career federal prosecutor whose first day on the job in his decade-long tenure as FBI director was 9/11/2001. He's very much a "just the facts" kind of guy. And Mueller knew that he didn't have a lot of time to thoroughly investigate and prove beyond a reasonable doubt a series of complex, transnational, and ONGOING crimes and issues of corruption, obstruction of justice, etc. - especially given how determined Trump, his administration, his surrogates like Giuliani, and apparently the entire Republican Party have been in attempting to undermine his investigation at every chance they get.
Fortunately, Mueller has hardly been the only individual involved in investigating Trump - or who will be investigating him further (get going, House Democrats! 
).
(Sorry, this is a bit of a meandering and possibly unclear post.)
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