Its not the penetrating that is the problem when Mark hits, its the overall damage bonus. I don't really have a suggestion because I don't know if you made any trade-offs or what PL you are, or where before picking up the extra PP.
Since it looks like your strike is already at rank 10 I would think about normalizing your trade-offs to being 10 across the board. After that I would think about pulling a Yoshi and taking teamwork a couple of times so that you can really boost other people on the team, Mark is pretty much a goon sweeper, he can lay waste to an army of minions in the blink of an eye, and he can hold his own against most equal villians, but against the bigger bads, he needs the rest of the team. Actually another thing to think about is upping your saving throws. Mark is wide open for pretty much any non-damage power. To save vs Fort or Will save power, he needs to roll 10+rank of the power, that is pretty bad. Kelly has a 0 will save, but that was purpousefully left as a weak point, not sure if you were going for that with Mark, I'd suggest that a +10 in saves is good since that gives you generally a 50/50 chance of saving, and prevents some of the worst effects of powers like insta KO from Fatigue, or Insta Death/Coma/Paralysis from Drain.
As a sidenote, your regen is off, it takes 6 ranks to get a recovery checkeach round without rest for both the Bruised and Unconscious conditions, its 3 ranks if its just 1 or the other.
Actually looking at your super speed, the damage values are a little off
Super-Speed +10 [cost: 5pp/level]
*Integrated power: Strike (+10 attack, +10 damage)
*Accurate (Strike)
*Rapid Attack (as strike above, 45 foot radius)
*Rapid Fire (ranged +7 attack, +10 damage, autofire applies up to +5)
*Wall Run
*Water Run
(Total pp spent in powers 60
Your jipping yourself of 10pp on the main incarnation
Speed + Quickness + Improved Initiative = 3pp/rank
Strike = 1pp/rank (you have another PP/rank to spend as the base power must have 2pp/rank for the PFs that you have)
Also, the damage for your rapid attack and rapid fire is too high, it makes use of the strike damage, but, they are APs off the strike so they cannot use its damage since they cost a full 2pp/rank themselves
Rapid Attack is really Area + Selective at rank 10, so thats 2pp/rank (+0 damage, 50ft radius) It would be better if you had a higher normal strength, or if your strike was outside of the Super Speed. Its still good for things like trying to disarm everyone at once, tripping everyone, etc, the iconic speedster stuff.
If you want to be able Rapid Attack everything and still have a high damage bonus, I'd make the Rapid Attack the default 2pp/rank power in super speed and use your 3PPs (plus 1 picked up from no longer needing to buy Rapid Attack as a PF) to buy
Equipment (1) Combat Gloves [Strike 4, PF: subtle]
Strike 3
The strike would represent hitting things faster = more force, and the combat gloves would be some gloves with weights in them to add more force to your punches, and next time he gets more PP he could up it some more. This is what my over all suggestion would look like:
Super-Speed +10 [cost: 5pp/level; 53pp]
*Integrated power: Rapid Attack (+7 damage, 50 foot radius)
*Rapid Fire (ranged +7 attack, +10 damage, autofire applies up to +5)
*Wall Run
*Water Run
Strike 3 [1pp/rank; 4pp]
*Accurate (Strike)
Equipment (1) Combat Gloves [Strike 4, PF: subtle]
I'm probably going to also grab 2 ranks worth of the Luck feat and considering Seize Initiative. Probably put the remaining points into saves (Will, probably) and then bank the rest (if any). I was considering giving her Inspire, since someone on the team needs to be a team player, but it just wouldn't work with a big blob of spiders inspiring everyone else to victory 
