Clearly I need to do a full analysis.
AP / Dura: Skulduggery by default, seeing as Fetus scales to someone who doesn't even have a profile, while Skulduggery casually blows holes in walls by flicking his hand.
Flight - both have it, but Fetus doesn't even seem to use it. He was actually jumping after Meat Boy up walls in the fight I saw rather than actually flying. Meanwhile, Skulduggery is no slouch with using his flight to get around, giving him superior agility and dodging ability.
Immortality - Skulduggery's aren't amazing, but type 2 can be useful if he ever does take a hit, Fetus needs to transfer his consciousness to another fetus (which we don't even know where it is) in an unknown timeframe, so it isn't applicable for this fight unless someone can prove it happens to a fetus that is already prepared for battle and close enough to immediately start fighting again.
Homing attacks - not likely to be useful, all they do is bend towards the target a bit, their homing ability isn't great. Skulduggery traps the projectiles in air pockets, or pushes air / throws fire at them and causes them to go off before they hit him.
Teleportation / BFR - Fetus doesn't seem to use this in combat at all. Didn't use it to catch up to meat boy, didn't use it to save himself from falling into a pit, didn't teleport meat boy into projectiles or traps, didn't teleport his projectives into meat boy, just didn't teleport anything in general.
Intelligence: Fetus takes the technological intelligence with all his machines, but I'm pretty sure Skulduggery is more intelligent in terms of fighting skill and strategy, considering he's a centuries old sorcerer who fought in a war and has practiced and trained in various fighting styles with some of the world's best.
All in all, Skulduggery should take this pretty easily. Fetus just fires missiles, which are easily countered. Skulduggery meanwhile flies around throwing fireballs and pushing Fetus around with telekinesis until the suit breaks.