This episode has some pretty severe continuity errors:
1) Claire's blood Not being used.
2) Dr. Surresh being a PHD and not a medical doctor.....something Surresh stated explicitly in a season past....yet Hiro/Ando sure treated him like a medical doctor.
3) I am pretty sure that in the first episode of season 1 you see a picture of Nathan in the army. Yet for this season finale....Sylar said "you claim you graduated first of your class at Annapolis"....hmm wrong service Acadamy, unless a Marine.
4) Sylar does not fly. Now we saw him, possibly levitate in with his TK power...but as to powers we have seen him take...flight is not one. Kinda hard to impersonate a flying man, that revealed his power to the chief of staff and Secret Service, when you can not fly.
Sure you can say he stole it empathetically during the fight, or from someone else...but that is incredibly poor writting.
5) The US Government already has an organization called "The Company". I'm sure the CIA is fine sharing with a bunch of mutated freaks
The sad part is you see the writting staff struggling to fix the show, but it just does not feel organic. People feel there is too much Sylar....trap the unkillable man inside the personality of another character. Nathan Petrelli the character has gone stale, lets add a bit of Sylar and suspense on when he will blow.
Intellectually, these are not bad plot developments in theory, but the execution is off.
Moreover, they just brought back the Overpowered Peter (

) Problem, if he absorbed all of Sylars powers. Hiro being allergic to his own DNA is an incredibly unsatisfying answer/situation.
Can Ali Larter not die and stay dead?
Honestly I think they should reboot the show, and go with the original plan, every season is a new set of Heroes. If the writing staff ignores continuity then you feel cheated and the writers do not know their own show. If the show repeats too many old story lines, or uses the same tricks, then you feel like the show is going nowhere and has no clue.
Reboot completely, or the writing staff had better map out a 2 season arc and not half ass it.
For those that want Heroes cancelled, it is an NBC/Universal produced show, which means that it will be unlikely to get the axe first as it is in effect an in house production....however if they can not even show the big fight...what type of budget restrictions is the show under if for the season finale throwing people already and some levitation is the order of the day.