I've never understood why these investigations take years, but I also don't understand the scope of what they're looking at. My hunch is Trump will be into his second term before anything comes of it.
The best analogy I can think of in a case like this is trying to hunt a particularly wily animal. You don't just run at it with a gun and hope you get lucky; you want to set up the perfect position, use the perfect tools, and wait for the perfect moment. It should only be a question of
when you catch your prey rather than "if."
Here, it's that Mueller needs an airtight case. Remember, he'd not only be taking on the President, he'd be taking on a President notorious for lying, obstructing justice and filing lawsuits. If there's even a slight weakness in the case, Trump's legal team will seize on it and try to make Mueller's life a living hell (I wouldn't rule out them suing Mueller himself out of spite). He also has to decide which actions are best at the state level versus federal, since we know Trump will try to pardon as many people as he can.
Hell, you've seen how Trump and crew have made false claims about attorney-client privilege and the data Mueller could use from the raid on Cohen, and that's despite the raid being entirely legal; imagine if there was
actually a hint of impropriety, or a hole in Mueller's chain of evidence. His team only really gets one shot at this, so it's better to be slow and methodical.