I think the Haitian is the reason Peter doesn't remember anything. I think he found him and Peter wanted to forget he even had powers. Peter was probably thinking he is to dangerous after exploding. So he probably had the Haitian wipe his memory to protect everyone from himself.
I don't know why Peter's memory was wiped, but it's obvious the Hatian did it (both from the nature of his ability as well as the fact that Peter is currently wearing the Hatian's necklace).
But if I had to guess, I would bet it's part of a more elaborate scheme. Peter might be working with Mohinder, Noah & the Hatian to bring down the company. It's possible Peter's mind was erased to hide details of the plan, or possibly to hide himself for a while.
If my little conspiracy theory is true, expect one/some of the lolIrishGangstas to have an ability, or at least be strongly connected to someone who does (maybe kindly irish sister/hot love interest?? HMMMMM?) In other words, part of me thinks Peter's mind was wiped and he was put in the "iPod" shipping container deliberately, to meet the very people who were told to hijack the shipment.
As for the X-men connection - mutant superheroes, there was bound to be some crossover of characters / themes. Heroes is heavily influenced by comics in general and x-men in particular.
Wolverine - Claire
Rogue - Peter (lol)
Cyclops - haven't met this character yet, unless maybe Ted Sprague
Kitty Pryde - D.L.
Jean Grey / Professor X - Parkman
Beast - sort of Niki/Jessica
Nightcrawler - Hiro (BAMF)
Storm - expect to meet a character who can control the weather before the series ends. I'll give 2:1 odds the actress is black.
Jubilee - fuck this bitch she was never a real x-man
And the Company, like Magneto, claims to be advancing the human race by protecting and advancing the interests of mutants, while excusing the means to their ends all the time and generally acting like dicks.