It completely depends... In the Matrix no? Normally yes. Neo has no real power just a computer programming idea... Yoda does have real power, and he could probably use it in the Matrix. The matrix depends on your willpower and shit and your power to believe. He believes in himself Yoda could pull it off in the Matrix because he could probably get more power then anybody else there. But then again so could Neo... In the Matrix its an uncertain thing, outside of it however Yoda kills Neo fast.
Then again inside Yoda could use the force to unplug neo 😛
This "Neo vs Star Wars character" threads suck. Sorry...but that are two different "realities".
Still:
- both are equally fast
- Neo can get wounded by normal weapons (that can be seen in Matrix:Reloaded) so a lightsaber would probably hurt him bad.
And please...Neo can't freeze people. He can freeze bullets. Still Yoda could force push him through a wall or slice him with his lightsaber.