It’s worth noting that 2000 was a very boring, sleepy election that only became (in)famous because of the Election Night results. If Gore would’ve embraced Clinton and put a little more effort into his campaign, Bush would probably be remembered today in the same vein as Dukakis. The FL thing would be remembered as obscure election trivia if Gore would’ve won AR, TN, and NH.
OTOH, Trump won his election through sheer energy and force of will. 2016 was also a much smoother Election Night for Trump than 2000 was for Bush. Despite going into the night as a greater than 2-1 underdog, he managed to wrap up NC and FL pretty quickly and painlessly, and turned several Lean D states into tossups pretty early in the evening. I think the 2000 results were affected by the coverage, whereas 2016 was going to be Trump’s night regardless.
I think Clinton's popularity in 2000 is vastly overrated. His personal favorability ratings were nearly Drumpf-level horrible and polling showed a majority said they didn't want "Clinton policies" continued. The problem wasn't that Gore distanced himself from Clinton but that he did so in an overt way (i.e., Lieberman, the music panic, the DNC kiss) that made him look cynical.
I also think Gore failed to realize that there were few, if any, voters who cared about Lewinsky but were pro-choice.