Why I think 3322 is a great setup:
Shadow Blade:
I was a strong opposer against anything not named metal blade, but after a while, I'm starting to realize that metal blade has some key weaknesses that make Shadow Blade more desirable.
First of all, if you want to use MB to its full potential, it's best to throw it on the ground, pick it up, and throw it at the opponent. You can do great combos, safely pressure and harrass. The problem with this is... it isn't a threat from long distance if the opponent is patient, and decides to catch it, or simply block it. In addition, when you have MB in your hands, your options become very limited, and can easily be shielded by a player who is smart and just anticipates your throw.
If you throw it regularly, not only is it slow, but the animation takes forever to complete, and the blade has a much higher chance of getting caught then the item version of the throw. It's also difficult to convert from this version because of the longer animation, and people can easily jab you out of your approach.
With Shadow Blade, it has none of these problems, because it's a quick lemon-ranged weapon with good hitstun, and is very difficult to punish on block. I strongly believe that because of this alone, it would help Mega apply safer and more efficient pressure as a midranged fighter.
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Danger Wrap:
Danger wrap is clearly the better option. Not only does it give Megaman some much needed kill power, but it stuffs Arial approaches, and most importantly, gives him a MUCH better defensive pivot option at close range.
Nothing sucks more than having your back to your opponent, especially when they are fast. The only moves you have to turn yourself around in the air are a b reverse Metal blade, and a crash bomb.
If your opponent is both smart, and sprinting, they could easily block your long animated crashbomb/MB, and convert it into a throw.
With Danger Wrap, the explosion at close range would not allow them to grab you, and give you actual hitstun that can help you reset the midranged neutral game.
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Tornado Hold:
By far his most intriguing recovery, because it gives Megaman better high recovery options, potential kill confirms off combos, unique edge guarding, and most importantly, better options out of shield.
When you're in shield, the best option as megaman is generally to grab because everything else he has comes out a tad slow (Fair), or is unreliable (Bair/Nair)
With TH, he could stuff smart players who space their short hop shield pressure, and potentially swallow them into a combo. If you miss, he could run away since they have to run through the tornado, and you could easily pivot using one of the two aforementioned attacks.
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Skull Barrier:
With this, I like this better than the others because of its shorter duration, and it's ability to reflect. You can destroy projectile characters, and not be locked into death if you have it out when you're off the ledge because it ends so quick. This is more of a personal pick, it I truly believe the other attacks are much stronger than his other attacks.