Hero: Future Peter's scar revealed?
It finally seems we got some answer as to how all the future incarnations of Peter we've seen can be scarred: if an injury is inflicted on someone with healing powers while the Haitian is around (or, presumably, if their healing ability is similarly nullified somehow) that injury will run its course like any normal injury, including leaving scars or even killing them, even after the force nullifying their healing power is removed. Peter was cut by Future Claire because the Haitian was around; later, when Peter was alone with Nathan and had access to his powers, it seemed that those cuts were still open and not healing.
Of course, if this is true, like most things on Heroes, it retroactively causes all kinds of problems, espeically with the first season as well as Claire and Sylar's perceived invulnerability. Bennet's stated desire to find Sylar's weakness and kill him is dramatically neutred when the audience knows that simply having Bennet's best friend stand next to Sylar while Bennet shoots him would do the trick.
But at least we know how Future Peter could have a scar.
Villain: Why didn't Hiro teleport out of his cell?
Once again, Hiro provides comic relief instead of using his power to teleport his way out of Company holding. The writers have said the Company has some kind of power-sapping tech in place for the holding cells (despite having shown some of the villains using their powers whilst in the cells) but a line of dialogue or two to that effect on the actual show wouldn't kill them.
Hero: Sylar's development
I'm never going to accept Sylar as anything more than a serial killer despite how hard the writers are trying rehabilitate the character (he's not that bad, he's warped by his ability). As much as I'd prefer Sylar to remain the implacable, unrelenting boogieman of season one who slinks away in defeat only to return for really big moments, Zachary Quinto is doing phenemonal work with the character so I'm not minding his increased and more nuanced role. The moral ambiguity on display is certainly fitting considering that so far this season has been all about moral gray areas and the blurred lines between hero and villain.
And just like last week's partnership with Bennet, even if I don't like the idea in principle, in practice I enjoyed the hell out of a repentant Sylar making waffles for his son while wearing a "hail to the chef" apron.
Villain: Peters needs Sylar's power?
Um, shouldn't Peter already have Sylar's power? Peter has spent more time around Sylar than half the people from whom he picked up powers. Suddenly Peter has to consciously absorb Sylar's power whereas before it was always an automatic subconscious thing? Or has he always had the power, and simply needed Sylar's help in understanding how to use it? Either way, a bit more explanation was needed.
Hero: A more complex post-apocalyptic future
I've already stated that I don't mind recycling the "prevent a terrible future from occuring" plot but I still appreciate the fact that this season's is a little more complex. Instead of the usual "don't explode" or "don't release the virus" we don't know EXACTLY what about the proliferation of super powers causes the world to crack in two, and thus, while destroying the formula to prevent said proliferation might save the day, something else might do it too. And of course, Future Peter and his butterfly effect show that preventing the future from occuring isn't as easy as stopping or allowing one specific event to occur. Plus, Peter's inadvertent triggering of the Costa Verde disaster and the subsequent announcement that a super human army is being formed makes this apocalyptic future much more complex and interesting than past ones.
Villain: Another mystery bad guy?
Maybe I read too many comic books, but at this point, the only way the revelation of whomever the mysterious bad guy trying to assemble the formula will be in any way surprising is if they are NOT someone (or a relative of someone) we already know.
Hero: Tracy's origin
After trying to recapture the "ordinary person discovering they have extraordinary abilities" vibe from the first season with stupid Maya (and, more successfully, Monica) last season and failing miserably, the show manages to hit that vibe again in the right way with Tracy. I also like that her reaction to her power has less to do with her having a power and more to do with the fact that she killed someone with it.
Also, this business with her being Niki's long lost triplet who recieved their powers via experimentation was interesting and looks to be tying into the main narrative soon, and also connects back to the first season plot point regarding how Linderman setup DL and Niki to give birth to Micah. For the first time, I actually care about a plot involving an Ali Larter character.
Villain: Too many formulas
I hope at some point the show claifies the differences, if there are any, between the serum Mohinder created and the one created by the formula everyone is after.
Hero: Cool ass explosion
Future Sylar's grief over his son's death and the subsequent explosion was a pretty awesome dramatic moment and a showcase for some pretty cool effects work.
Villain: Where'd Sylar get that power again?
Are we supposed to assume that at some point between the present and the future we just saw Sylar takes another person's radioactive powers? Because the one he got from Ted in Season 1 should have been wiped clean last season.
Villain: Why did Hiro dig up Adam?
He teleported him into that coffin; couldn't he have just teleported him out?
Hero: Creepy future Mohinder
Present Mohinder is still a moron but I did enjoy the creepy future Mohinder who seemed more snakelike than the insect-like transformation his storyline's Fly homage was previously suggesting. It was also the first time a power was suggested to have an adverse effect on someone's physical appearance (ala Nightcrawler or Beasts blue and furry appearances than set them apart from regular humanity). In fact, Mohinder's idiotic drinking of his own mutagenic formula and subsequent transformation could be taking a page from Hank McCoy's book and his transformation into the blue and furry Beast we all know and love.
Villain: Why is Hiro digging up Adam?
Hero AND Villain: Parkman's animal totem
That Parkman's animal guide is a tortoise seems sadly fitting. Of course, it probably also means it'll be awhile before the slow moving animal leads Parkman back to the rest of the cast.
Villain: Uh, Petrelli boys? You have many, many powers. Use them.
Between them, Sylar and Peter have about 105 different super powers. Yet when they're attacked in Future Sylar's home they woefully used very few of them when fighting back. Instead of using Knox's power against him, Future Sylar could have frozen him in place with his telekinesis or bellowed at him with Jesse's sonic power. Peter could have stopped time the moment the hostage situation presented itself, then used TK on the reduced-to-normal-speed Daphne. Or teleported little Noah out of harm's way. Or, after the explosion, Peter could have just gone back in time to intercept Daphne, Claire and Knox enroute to the confrontation and averted the whole disaster he whined about causing in the first place.
Hero: Nathan's reaction to his situation
I'm pleased to see that Nathan's religious experience is being handled with a more subtle touch than its initial introduction suggested. I'm okay with scenes of him praying and asking for guidance but I'm glad they're tempered with his skepticism of Linderman and the fact that he isn't automatically fully embracing this whole "angel" notion. He also showed an awareness of the world he's found himself in (something the other characters show far too often) when he told Linderman he knows there are people with the power to allow Nathan to interact with the image of a dead man.