Any Greninja's around here want to give me some MU experience against my Villager sometime online? I lost to a good one at a tournament a few days ago. Sorry if this is the wrong place to post this.
EDIT: As Elu so graciously pointed out, I completely misread your post. I thought you were asking for help
against Villy, not
as Villy. That's what I get for checking Smashboards on my phone while I'm still in bed at 6:00 a.m. Either way, this is what I think while I fight Villager, so maybe this will be helpful to you from the other way around...?
A weak Shuriken will blow up Lloid rocket, but not when Villy is riding it. Jumping over Lloid is usually preferable to shielding, as it puts us in a better position (just watch out for Utilt and Dtilt), but be sure to mix it up.
Never let Villager get on a platform above you, because he will bowling ball your face. If he goes for a bowling ball edge guard, you can shadow sneak behind him--but MAKE SURE you get behind him. If you misjudge and get caught by the ledge, you are likely to get hit. You can also Sub on the bowling ball if you're feeling lucky.
If he plants a tree, camp til it's gone (but make sure you know when he pockets your Shurikens) and wait for him to come to you--and watch out for the axe. If you want to bait the Tree drop for a Substitute, go for it. They will chop the tree as soon as they think you're dumb enough to run into it.
Bairs off the ledge can do a good job of edge guardng him--they won't kill, but you can cycle 3 or 4 bairs and ledge re-grabs for good damage.
If Villager runs off the ledge, he is likely trying to Double Jump Slingshot you. Shield it or be ready to substitute off of it.
Usmash beats his Down Air, but it's close. If you don't sweetspot it, you'll get turnips in the face. Uair does NOT beat his Dair, and his Dair comes out very quickly, so your Uair followups should be conservative.
...that's all I can think of right now.