I know this is blasphemy, but in a 1v1 fight, I'm gonna give it to GO-TO.
Hear me out.
Stealth + Droid = VERY dangerous enemy for a Force User. They cannot sense his movements through the Force because he is not alive, and they cannot see or sense him due to the Stealth Generator. GO-TO would get frist strike and the element of surprise.
Darth Plagueis lacks precognitive abilities due his maxi-chlorian infection. If GO-TO were to make a strike at the Sith Lord from behind, without exiting stealth, mind you, Plagueis would have to rely on reflexes. This attack could come at any time, GO-TO could be his own assassin, or he could do this when (if) Plagueis boards his ship. But sometime when the Sith's defenses are down.
Here's what I see happening: GO-TO goes into stealth as Plagueis comes near. Totally unable to sense the droid, Plagueis is completely unaware of GO-TOs presense and, coupled with his lack of precognitive abilities, he is unsuspecting. GO-TO then sendings a paralyis dart at Plagueis. Mind you, these darts are used by assassins to be silent and quick, and if GO-TO is in close range, which he very well could be, Plagueis would have no time to react. Or, if you argue he could, GO-TO could literally float up to the Sith and stab him with a needle.
As someone else pointed out, Plaueis died in part due to poisoning. With his complete invisbility and Plagueis's lack of precognitive abilities, GO-TO could do the same.
1v1 = GO-TO?
Except Plagueis was pretty much invisible as well. Maybe not TRUE invisibility, but he was able to sit around on Coruscant without even Master Yoda knowing he was there. He would have to literally walk into the Jedi Temple and say "Hey I'm a Sith Lord here to kill you!"
If Yoda and the entire galaxy couldn't see him, what makes you think G0-T0 can?
Plagueis isn't really a hands-on kinda guy. If he has the tools to take G0-T0 out, he will use them.