For intangibility, since the trapping it lists are things like a mist, a ghost, a swarm of insects, he'd be intangible but not invisible. So security personnel and devices could still detect him, and if he goes too far in, once he becomes corporeal he'd presumably be separated from the rest of the party, making it a lot tougher of a fight. Also, maybe some situations will effect his spirit roll he has to make to phase in and out...
Plus remember that you can also choose attack forms that still work against intangible characters (depending on the trapping), (its in the Vulnerabilities section for intangibility)
As for the other one, I'm assuming its Infection, which still requires a successful touch attack, and a failed vigor roll.
With extras it wouldn't really matter too much, since a successful enough attack would take them down anyway, its pretty much just an attack trapping at that point.
The biggest difference is that a touch attack gets +2 on the fighting roll, so maybe either house-rule that away, or give selected villains +2 parry vs touch.
So, for wild cards that go up against him, either make them robots, etc, or people with high parry and a decent vigor, then at least he'd have to work with the party to get the jump on the guy and get the right attack bonuses, so he's not just mowing through everything by himself. (What I'd do is basically have a recurring villain who tends to go against him, everyone needs an arch-nemesis, basically a guy who uses voodoo and can transfer effects to his minions or people he marked, so he runs in, death-touches the guy and it succeeds, he expects the guy to drop dead, but instead one of the nameless henches go down, guy turns around and smirks and stabs him with a voodoo needle or something [or while I'm stealing from One Piece already, have him turn into a giant straw voodoo doll too])
Also, dont forget the GM gets bennies too, so maybe save those for re-rolling vigor rolls for insta-death.