There are a few rules (including Mega-Attributes and nova powers) I've rewritten from the ground up, while others I've merely tweaked or clarified. See what I've done, and feel free to comment or ask questions. Also, see New Quantum Powers; my revision of the Shapeshift power is there.

General Changes
Four-Color Combat: While almost no one ever dies in comic books (and if they do, it's only temporary), it's pretty darned easy to die in Aberrant. It's a gritty system in this respect, but some Storytellers may want to run a less "realistic", survival-friendly setting, where (for example) the Hulk can throw tanks for miles but manages not to kill Captain America or "baseline"-level characters when he hits them. Below are several options for this sort of setup. Be forewarned, one or more of these options will almost certainly stretch combats out, as characters won't go down very quickly.
♦ Double the recommended soak values for Stamina (Sta x1 for lethal, Sta x2 for bashing).
♦ Be stingy with lethal damage. Charge more nova points for powers that inflict lethal damage, or halve the damage die pool for lethal attacks. Or, assume all lethal attacks inflict bashing by default, and require a Quantum point be spent every time the player chooses to inflict lethal damage. Ruling out the very existence of aggravated damage in the chronicle is a good idea, as well. This will encourage players to use bashing attacks when possible.
♦ Make damage easy to heal. When a character is suffering from health levels lost to bashing damage (and is conscious), he may spend a Willpower point and make a Stamina + Endurance roll (Mega-Stamina may be added to this roll), at +1 difficulty; each success allows him to instantly recover a level of bashing damage. Basically, the hero (or villain) taps into his reserves and keeps going. This will lead to a lot of fights where people get knocked down, and get back up to suffer more punishment. This is right in line with comic book physics, though characters aren't invincible and their resolve will eventually wear down.
Lethal damage shouldn't be nearly so easy to heal from, but lenient Storytellers might allow characters to recover one level of lethal damage per day if the chronicle features a lot of action.

Extras: Characters can buy extras for Level 3 Quantum powers, or more than one extra for Level Two powers. For every effective level above 3 the power is, increase its nova point cost by 2. For example, a Level Three power with one extra costs 9 nova points per dot. When buying extras with experience points, increase the power's experience point multiplier by 2 for every effective level above 3 it is to calculate exp costs (using the formula given on pg. 230).

Limitations: The effective level of a power can be reduced by taking limitations on that power. Examples: Marvel's Sandman can only use Sizemorph: Grow when standing in an area with a great deal of sand, as he must draw the sand into him to expand. Cyclops' Quantum Bolt eye beams has the limitation "cannot be cut off" (and the free power characteristic; see below).
Characters can have limitations, as well. Classic examples include Superman's vulnerability to kryptonite and magic, the Green Lantern's inability to affect anything yellow with his power ring, and the Hulk's stupidity. This yields players more nova points to build their characters with; the nova point value of a limitation is up to the Storyteller, though a rule of thumb is 1 or 2 nova points for a minor limitation, around 4 points for a moderate one, and up to 7 for a major limitation. (Those who play other White Wolf games are familiar enough with Merits and Flaws to apply the same concept here.)

"Free" Powers: By spending double the number of nova points on a Quantum Power (including extras), or double the nova points on a Mega-Attribute enhancement (typically 6), the power/ enhancement costs no quantum points to use. The Storyteller is the final arbiter of what powers a character can use this option with; some might feel the ability to throw tanks into orbit or regenerate aggravated damage for free might be a tad overpowered. Powers with a variable quantum point cost (such as Clone, the Enhanced Movement enhancement under Mega-Dexterity and the Lifter enhancement under Mega-Strength) are assumed to have spent a number of "free" quantum points equal to the level of the power to determine the power's effect; any effect beyond this must be paid for by quantum points as normal.

Bonus Health Levels: Here's a new way to do health level bonuses gained from Mega-Stamina, Sizemorph: Grow, and Body Modification: Extra Health Levels, that gives die pool penalties more consistent with normal health levels. The first bonus health level added to the damage track is a Bruised level, the next bonus level is a Hurt level (-1), the third is an Injured level (-1), and so on, with health levels added down the track until Incapacitated. After this point, the next health level is a Bruised level, and additional health level bonuses are added down the track in the same order.

Enhancements as Powers: At the Storyteller's discretion, a player may buy certain enhancements for a character without the corresponding Mega-Attribute, if having the power without the Mega-Attribute is feasible. Such enhancements cost 5 nova points, and when the power uses the Mega-Attribute to determine effect, the character's Quantum rating is used instead. For example, Reed Richards of the Fantastic 4 isn't particularly dexterous, but has the Flexibility enhancement as a power. Since he doesn't have Mega-Dexterity, he can expand his limbs six meters for every point of Quantum (having taken Flexibility three times).

Mega-Attribute Changes
Mega-Strength: The old Potence vs. Fortitude setup again: offensive powers are superior to defensive ones. What is it with White Wolf and Strength-related powers? Anyway, I disregard Mega-Strength's listed automatic successes. Novas with Mega-Strength gain the same bonuses to Strength/ Might rolls as other Mega-Attributes do (which is in itself pretty awesome). Plus, to make up for toning down the power, the nova gains a number of automatic successes equal to his Mega-strength to Strength/ Might rolls and close combat damage dice pools. This allows more comic-book style combats, with bricks pounding on each other for extended periods of time.
(Don't complain too loudly. Taking into account extra damage dice from additional successes, and the fact that many Aberrants do lethal damage with their physical attacks, and equal ratings of Mega-Strength and Mega-Stamina, damage still comes out on top of soak most of the time.)

Quantum Power Changes
Clone: Clones created by this power have the same statistics as the original, with the exception of the following traits: Quantum rating, Mega-Attributes, and Quantum Powers. Each copy (plus the "original" nova) suffers a penalty to the following equal to the number of clones created: Quantum, levels of Mega-Attributes, and levels of Quantum Power. (Mega-Attributes reduced to zero or below do not penalize the corresponding Attribute.) Furthermore, the original's Quantum Pool (after the adjustment for lower Quantum and use of power) is evenly divided among each clone and the original; fractions are rounded up and remainders are added to the original's Quantum Point total. (For example, Deja Vu has a Quantum of 6 and Quantum Pool of 32, and creates three clones of herself. She and her clones now have Quantum ratings of 3, all her Mega-Attributes and Quantum Powers are reduced by three levels, Deja Vu has a Quantum Pool of 7, and each of her clones has a Quantum Pool of 6 (32 minus 6 for lower Quantum is 26, divided by 4 equals 6.5).

Mental Blast: Going on the description presented in the book, mental blast attacks the mind, not the body, and I can't see how having Mega-Stamina or being bigger protects your brain. Thus, every success rolled on the Intelligence + Mental Blast roll removes one point of Willpower from the victim, instead of health damage. Another option is to use a standard health level track, and use Willpower to determine "soak" against Mental Blast damage.

Sizemorph: Grow: Each dot of Grow adds 1.5 health levels and 1.5 dice (instead of one health level/ die) to others' die pools to attack or sense the character; round fractions up. For example, Grow 2 adds three health levels and three dice to others' dice pools to hit him. This reflects the enormity of characters with higher levels of Sizemorph: Grow, without making such characters too powerful.

Shapeshift: I've made some pretty extensive changes to the Shapeshift power -- in fact, I've converted to several powers. In exchange, I've boosted the effect of the powers, allowing players more flexibility and power when determining the capabilities of their characters' alternate forms. It's easier to create characters with this system that fit those characters of comic book lore that assume a form or particular class of forms, or such as the Wonder Twins and lycanthropes. Very few novas can turn into just anything; they'll have to buy different versions of the Shapeshift power to do this. See New Quantum Powers for my Shapeshift powers.