Across
3. maia: The Maya was an ancient civilization. Without question, (why? or y?), and adding "I" gives you maia.
4. Malson: Mal is spanish for bad, and a son is a male child.
6. Nose: Nose's old nick was Grundle_Brush, and another word for grundle is taint.
7. Strike Reyhi: Hitting is striking. A quasar is a ray from the center of a galaxy, and waving hello is "hi".
8. Holkeye: An eye is an orb. The Hulk was green, but oh (o), without you (u). Replace the u for an o.
10. Nightwolf: A arctic fox stalks it's prey after dusk, which is night.
12. NAMKCOR: In the Megaman games, when you get a weapon the screen says, "Get equipped with..." Rockman is Megaman's Japanese name, and Rockman backwards is Namkcor.
14. Arrowone: The first (one) projectile (arrow). Pretty self-explanatory.
15. DrSword: Doctors perform intubations, and cutlery is knives/swords.
17. Falcon: Falcons swoop to attack prey, and the new is because we all know how Falcon loves newcomers.
20. ModernAlgebra: Euclid was the founder of geometry, which is a school of mathematics, along with algebra. The successor would be modern.
22. Nouman: The new man comes after the old guy.
25. Chewey: Nougat is chewy, and the bonus ecstasy is an extra "e".
Down
1. Irock: The short name for Richard is Dick, and a space is a gap. A dickgap owns his face.
2. Silverline: Mercury is called "quicksilver", and a segment of a plane in geometry is a line. This leads to Roph's old name.
5. Leventhan: Rather's partner is "than". When you add yeast to something, you leaven it. "Than" after "leaven".
7. Skanker: A promiscuous woman is a skank, and if it were an adjective, to show more of a skank it would be skanker.
9. LadyJ: A "jay" is a blue bird. A female is a lady.
11. HaloOfTheSun: Sol is another name for the sun. A diamond sits on an engagement ring, and halo is another word for ring. Thus, Sol's ring would be the halo of the sun.
13. Kitkatkan: "Give me a break" was the slogan for KitKat bars. The can is the "kan".
16. Zylos: Zylos is the arctic fox philosopher. Vulpes is the genus of foxes, and philosophy is existence theory.
18. Starfyre: Immolating means setting on fire. The heavens are the stars. "Without I" removes the "I", and the question "why" adds the "y".
19. Garygill: The Ambiguously Gay Duo was made up of Ace and Gary. A gill is part of a fish that allows it to breathe under water.
21. Arlen: This might be hard to get if you don't know arlen's "full" name, which is arlen reyb. Arlen wouldn't have babies, he'd have reybies. Thus, rabies.
23. UHN: An old forum joke, which at one point was word-filtered to "SEX" (Pretty obscure :3)
24. Anski: "A" and "an" are indefinite articles in speech. A winter sporting good is "a ski", so if you use the wrong indefinite article, it becomes "An ski".