Man, I just made this EXACT choice a month ago.
I priced out both, and with identical options the Bu ran about $6.5k over the SSV.
Just looking at the boats, the Malibu seemed to have a plusher interior -- vinyl covered dash, billet plaques, "Isota" steering wheel, slightly thicker seats, etc. I don't see how you could make a nicer interior than a VLX has. On the downside, my wife thought the vinyl dash and stuff was just one more thing to take care of, to crack in the sun after a few years.
On the Supra's side, I liked the tower better, and it just seemed twice as big inside for some reason, even though it was only 8" longer and 2" wider. It seemed a foot wider, and has the stadium seating option which rocks.
I also liked the Supra's soft ballast bags, which are easy to upgrade, and take up almost no space when they're empty. Being a "family man" I spend a lot of chill time, so the extra space is nice when we're not going big.
The Supra's playpen bow seating is also super cool, and gives you a HUGE "Basement" area underneath for storage, or a mondo ballast bag.
The local Supra dealer treated me MUCH better though, and offered me way more for my trade, which sealed the deal for me. I couldn't justify > $6k for the (slightly) nicer interior, and what seemed like much less space.
To be honest I loved both boats. I'd have been happy as hell with either. Who knows, I might have ended up with the Malibu had the dealer done me right. I gave him first chance -- visited him first, and LOVED the VLX, but he acted like he was doing me a favor selling me a boat, whereas the Supra dealer seemed very eager for my business.
As for wake comparison, I've never ridden behind a Malibu, so really can't make an honest comparison. The wake my SSV makes is killer though.
I couldn't be happier with my choice at this point. Sometimes things just work out.