What crimes have anyone been indicted/convicted of that is remotely related to being in cahoots with Russia?
Well, there you have it. "Cahoots" is not a crime. The president will not be charged with being in "cahoots."
Flynn's phone call to the Russian ambassador, as incoming NSA wasn't illegal.
That's to be seen. What was the call about? It was intercepted and red flags went up for some low level intercept operator, who reported it to his/her supervisor, who in turn run it up the chain. When asked about contacts with Russians, Flynn didn't say "Yeah, I talked with the ambassador a few days ago. Just getting onboard, ya know."
No, instead, Flynn lied about it. He denied it. Why?
When informed of the FBI's concern, Trump took a couple of weeks to think about it before firing Flynn.
Then Flynn is charged. In a plea deal, Flynn pled guilty and apparently has been cooperating. But, he made a plea deal, according to you, for doing nothing wrong.
One of the problems you have is that crimes have been committed, as evidenced by people pleading guilty rather than mounting a defense. Another problem you have is that Mueller is using their guilt and potential punishments as leverage to uncover evidence of other crimes, perhaps by other people. A third problem is that quite often investigators ask questions they already know the truth about. Lying to the FBI or to Mueller investigators is a crime in and of itself. That's what crossed up Flynn. There's no telling who else got snared in that web.
Your biggest problem is that Mueller has been running a fairly tight ship, not leaking very much. We really don't know what he's got. It is possible that the report will say something to the effect "We looked everywhere for almost two years and we found that Trump is as pure as the driven snow. This was a big nothing burger."
On the other hand, while it may not directly implicate Trump in coordinating with Russia on the campaign, if Trump and/or his companies are found to be money laundering or tax evading for bad players, Trump could very well face some serious legal jeopardy following his presidency. Unless, that is, you're of the opinion that as the last act of his presidency, Trump could constitutionally pardon himself and his entire organization. That still leaves the issue of NY state charges. He can't pardon himself there.
And I can hear you now, as Trump is led in cuffs to the prison van, "See? I told you there was no collusion!"