I'm glad they didn't stick with the terrorist storyline, it would've been too intense for an introductory of a new show, considering there are plenty of other shows out there that deal with terrorism head-on and Heroes isn't one of those kinds of shows. Besides, the connection of a man with radioactive abilities and him being in a terrorist group would've been too obvious. Although, I have to say the setup was certainly interesting. Then again, too powerful and intense for a pilot episode. The show does have the prophecy of the explosion in New York and some mentioning of terrorism here and there, but it's not blatantly obvious like what was shown here. I'm not saying that there aren't people in such organizations or situations that won't have abilities, but Heroes essentially is a show about hope, and having a terrorism tie-in wouldn't really give the audience much comfort in that regard. So yeah, I'm glad that got replaced with the Ted Sprague storyline.
Though, another tie-in was Matt Parkman. Originally he wasn't introduced until the second episode, with the Walker family crime. The unaired pilot showed him finding a hiding terrorist from hearing his Arabic thoughts instead of Molly Walker hidden away in fear. This also shows that Matt wanted to be on the S.W.A.T. team instead of becoming a detective, which is plausible if they'd kept with the terrorist storyline. I find it interesting that they kept how he approached his abilities in both versions: on a crime scene, hears the thoughts of someone, enters crime scene without authorization and finds the person hiding, but ends up getting questioned for his act of heroism. So they had the idea of what to do with Matt's character from the start, it was the matter of getting the right storyline in. Also, I liked the surprised interaction between him and the radioactive man. They knew each other, and now we'll never know how or why.
There was also the trouble with Matt's marriage, which seemed a bit more unbearable for either of them as they were going to marriage counseling. Watching this, I've concluded I like his current wife better than the original one. But then again, I've always liked her on the show. She does have her flaws but overall is sweet and supportive of Matt, whereas this woman seen here is just bitchy.
Now, there's the Sylar storyline, which I have to admit freaked me out. I knew that they originally wanted Sylar to be a middle-aged man who was deeply religious and once being contacted by Chandra was conflicted and questioning whether his ability was a gift from God (or the Devil) and started using it for that purpose. But actually watching it all unfold in this really made a different impression on me, because as soon as Mohinder walked (er, more like broke into through the window) into Sylar's apartment I just...I was like "whoa..." Definitely different from Gabriel Gray, which I am SO HAPPY they changed Sylar's storyline. And in the end with Mohinder about to leave and then suddenly a dark-claded figure with a hat stood before him, and Mohinder uttering the word, "Sylar" in somewhat surprise and fear...I freaked the hell out. Seriously, it was a "FRAK ME!" moment, the same with the audio-recording of Sylar and Chandra talking, again completely different from their interaction we see later and just the deep and hoarseness of Sylar's voice really scared me (besides, we now know why Chandra called him Mr. Sylar, because originally his name was supposed to have been Paul E. Sylar, not Gabriel Gray who just took the alias from the watch he'd been working on. Really changes perspectives on things, huh?)
I liked, however, that they kept the religious undertone with Sylar's character, as we revisit that scene with the "Forgive Me; I have sinned" writing in blood in the third episode when Mohinder and Eden enter his apartment, then again with he visits his mother. It's still there, just subtly, which I think was a good thing. Adds the complexity of his character I think, instead of letting it known that he is just this whacked out religious dude trying to justify his actions on God.
Other than that, nothing much else was changed. There were some extended scenes as seen in the pilot episode we know, such as Peter's dream featuring him falling off the building and Nathan appearing there (which would've given it away from the beginning), an extended conversation between Claire and Zach along with Claire seeing the truck with terrorist hidden inside, which had to be taken out because that storyline was being cut indefinitely from the show; more of the Simone and Isaac interaction, including him going cold turkey from using the drugs and later cutting off his own hand. There was also a minor change with the Sanders' scenes, mainly Micah taking $300 and leaving to visit his father in prison, although they decided to not go that route.
Yeah, so the unaired pilot really was interesting, and makes me wonder what kind of show it would've turned out to be if they'd stuck with the things they didn't change, especially keeping the original ideas for Sylar and the terrorist storylines in particular. The show would've gone in a completely different direction, and I don't know whether good or bad. They had some heavy religious themes, and I don't think it would've been recieved well by audiences. It was interesting nonetheless, but still I think too intense for a beginning episode and thankfully they tamed it and took out the unnecessary points which would've been questionable. Because really, there are so many terrorist plotpoints in other shows as I mentioned before, that it would've been cliche to add it to Heroes.
But that's just my opinion, anyway.