So I've never been a Sailor Moon fan, made sure to open up Usagi's page to check what she could do before responding at all, proceeded to have a minature heart attack with how many sub-tabs and keys she has...my god.
Anyways, the Transmutation thing is kinda wierd. Isaac and the gang were going to be turned into a bunch of trees via magic, or psynergy, or something (GS' power system is all over the place and has more than one type of 'power' in the verse) and because Isaac's Psynergy(?) knew he didn't have a way to protect himself or counter it, it just made a forcefield sort of barrier all on its own to stop the attempt to transform him. So his powers are semi-aware and if Isaac can't do something about a sitaution (like being transformed against his will) it will at least TRY to auto-save him.
This power was only briefly talked about, only briefly showed up, barely explained, and completely out of left field. So...yeah, that's the best I got.
As for the Moon Sword, no idea if Isaac has a way to stop that from happening, honestly. Seems kinda like an EE, but I'm not familiar with Sailor Moon to be sure. If that's the opening move or Usagi has Isaac pinned, that might be a easy win con unless I've forgotten anything.
In Isaac's corner, though, his main element does let him control insta-kill Soul, Curse, and Death manip moves, which Usagi doesn't seem to have a resistance to up to Princess Serenity (and I don't know if the Silver Cystal can protect from those kinds of manips, the single manga page I found doesn't give me much to work with here, so correct/update me). Isaac's other elements would also have useful effects, like Jupiter letting him Power Null, but they won't be his first choice, so he probably wouldn't dip into using something like that unless he had a bad feeling about this or Usagi's abilities unnerved him enough to say 'Yeah, no."
Usagi's resistance to Status Effects is also wordded a bit weirdly. It seems like she's at least immune to blinding effects, but I don't know what all to extend that to. So for now at least, I'll lean off Isaac's Poisons, Sleeps, Stunning, ect, all those statuses he has.
Isaac bringing the Djinn to the party, though, is what makes this one interesting, and makes it hard for me to make a good call. 'Djinn Spam' is a pretty common tactic in Golden Sun, so much so that late-game enemies have powers dedicated to trying to stop the gang from doing it. The Djinn are all basically little creatures fused into Isaac that he can use for summons, for all sorts of powers, and switching out abilities...and he has 72 of them and they all do differant things. Rime and Luff both also Power Null, a handful of them make forcefields, even more of them change around stats (all of them, they can boost Isaac's AP, Durability, Speed and reduce Usagi's), Kite can boost Isaac' action/reaction time, Serac and Whorl both have insta-kill effects, Ground and Petra both immobilize, ect. Isaac has all of them at the ready, and there's no cost to using the Djinn for support like using Psynergy (though, being on HIS Lighthouse means he'll probably never run out of Psynery either), so they're entirely possible as spammy opening moves and can have all sorts and nasty effects that would set Usagi back. Power Nulls and Speed Manips are probably the worst, Usagi seems very reliant on powers and Golden Sun's Power Null seems to knock out nearly everything, even some level of physical techniques, so she'd be in a bad spot. And with speed equalized, it's bad news that Isaac has speed manipulation powers and Usagi doesn't seem to, using the Djinn or Psynergy to speed himself up and slow her down, and improve his reactions, means Usagi's going to lose ground fast if he uses any of those.
Also, some super unlikely things Isaac can do but they COULD help: The Mold Djinn compells a victim to either attack thier allies or, if there are no allies, themselves. We're not sure if this is some sort of bloodlusting/beserking/confusion effect or mind control, so Usagi might resist it anyways, but it's there. Another Djinn, Lull, briefly stops fights, making all of Isaac's oppoents temorarilly non-hostile, if just for a small amount of time. Again, we don't know if this is mind control or not, so no clue if it'd actually work. Isaac also has summonable allies. I know it says 'no outside help' but he does have a power to, for example, raise the dead or demons to fight for him, so not sure where that lies in a grey area. But if that's allowed, those could be distracting extra targets that need dealing with too. So those are some pretty unlikely powers, but they might be useful as distractions or ways to disrupt Usagi from actually engaging Isaac himself to buy time.
All-in-All...I have no idea currently. I know too little about Sailor Moon for this one. It seems like Isaac has a lot of really useful abilities to fight Usagi, and at least one way to avoid one of her easy insta-wins, but I still don't know about the Moon Sword's EE, if she'd use it really quickly, and if Isaac has anything he can do about it. I think I've left all the good, relavant information here about Isaac's best options and possible opening moves and will wait until I know more about Sailor Moon before voting.
EDIT: Embarassingly, I misspelled Usagi as 'Usami' this entire post...whoops!