Hyper Ability:
There are a number of factors that determine how much damage a hyper attack will do. The factors that change the amount of damage are:
Users Statistics: Higher values of power and energy mean more damage is done, period. This is the most important factor by far.
Victims Statistics: The victims stats can effect damage as well. The victim's defense reduces damage if the value is higher than the users power + energy value and more damage if lower. Also, some hypers do more or less damage if a stat is in a certain range or if the victim is a certain ratio.
Number of Hits: The number of hits a hyper deals also effects the power. In general, more hits means less total damage, but if the move is blocked the chipping damage is higher. Fewer hits deals more total damage, but do little chipping damage.
Cut Away Attacks: Closely related to Number of Hits. Cut Away attacks only count the hits before the cut away. For example, even though Wolverine's Weapon X move is 12 hits, it only is counted as 1 hit for purposes of damage.
Area of Effect: The larger the area of effect, the less damage a move does. By this factor, Iron Man's Proton Cannon does less damage than Ken's Shin-ryuuken, which shoots straight up.
Blocking Restrictions: Some moves can only be blocked in certain positions. If a move can be blocked standing, crouching, or jumping, it does normal damage. If any or all of these positions cannot be used to block a move, less damage results.
Hyper Speed: The faster a move is the less damage it does. This includes starting time, quickness of hyper, and recovery time. Slower moves are more powerful. War Machine's Proton Cannon is stronger than Ryu's Shinku Hadoken because the cannon has a longer starting and recovery times.
Number of Vigor Levels: Some moves take more than just one level of vigor. The more levels a move takes, the more damage it does. For example, Akuma's Shun Goku Satsu costs 3 levels, meaning it is powerful than his other hypers, if only this factor was considered.
Combo-ability: The easier a hyper is to combo with Chain, Sweep, and Air Combos and with specials and even other hypers, the weaker is it. Moves that cannot be comboed are more powerful. This includes how well the move works for Team Hyper Attacks and Hyper Chaining Attacks.
Special Penalties: If a move leaves the user in a vulnerable position after or during the hyper (For example, Jill's Star Cannon attack), the move does more damage.
Variety & Length: Applies mostly to hypers that increase the user's stats. The larger the variety of stats increased, the less the total effect will likely be. Also, the longer these enhancements last, the weaker they will be. Therefore, an ability may +2 to all stats, or +6 to a single stat, with the + 6 giving a more dramatic and noticeable improvement.