I know this is going back a bit, but I've been wondering what was so wrong about the future in Season 3? Future Peter brought Present Peter into it and started saying how everything was bad, but I didn't see anything particularly depressing.
The only problems I could see were the explosion in Costa Verde, which was caused by Pete messing about with the timeline, and the various terrorist attacks in the related comic, which again were the fault of Pete. The only terrible thing about that future seemed to be that peter was getting a bit jealous of everyone being special, not just him...

There was also the fact that specials who didn't work for the government were being hunted, put into camps, etc. Future Peter highlighted that in the first episode, but I'm sure that's only a minor dealio.

Yeah, it's a bad future because the specials were being hunted and, for lack of a better term, used as guinea pigs for what I guess was new and more powerful serums/better abilities to market.

In every future we've seen, the specials have been hunted or, in some way, the cause of the bad future. Only real future that I don't remember specials being hunted in was the virus future, and that was only because the world's population was killed off almost entirely.

I thought that future was bad because the world was going to explode...?

It was both, really. Peter wasn't focusing on that in the first ep when he plead to Claire, though. He said he could go back, before the hunting, make it so there was no more camps, no more experiments, etc.

Now, hold on a minute, here- I believe we saw two different futures in Season III. The first one (in which Future Claire tried to shoot Future Peter before he teleported) did involve Specials being hunted by the government, but there was no indication of this the second time we saw the future (when Present Peter traveled there), particularly given that all kinds of everyday folk were exhibiting (presumably formula-produced) superpowers on every street corner, apparently without facing any manner of persecution. In this one, the only reason explicitly given for seeing any apocalyptic overtones was the "world-is-going-to-be-blown-in-half-for-some-reason" bit.

Claire had the Pinehearst pin, meaning that Arthurs organisation won in a bad way.

Normal people, people who were originally normal but capable of purchasing for themselves an ability, were clearly not persecuted. They were merely consumers who bought a product and used it.

Actual special people though. They can't be contained and, for various reasons, are clearly dangerous. An ability in the wrong hands can and does have disastrous effects. People who are born with the genetic marker that signals they will have an ability, no matter what it is, would be scary to a world that only knows about the cutting edge work that Pinehearst does. People won't like the fact that anybody could have a power and that the dangerous kid down the street might be able to blow up a house simply by using his mind.

Real specials would be scary as all hell for a normal world. Through Pinehearst, abilities can be regulated and controlled. It's easy and simple and people get what they want. That's why people took to Pinehearst's serum how they did in the future. It was controlled and did little harm. With real specials, just like we see in the show now, people don't like what they don't understand. Specials are different from the rest of the world. They get persecuted no matter what.

You can also say that Pinehearst was experimenting on and researching specials to create bigger and better serums. Keep them out of the public eye, create a better product to sell and make a profit from, and everyone is happy.

We may not have seen Specials get persecuted in the future(s), but that doesn't mean it didn't happen still.

It really all boils down to a few simple rules:

1. Humans FEAR what they do not understand.
2. Humans KILL what they FEAR.


And the corrolary rules:

1. Scientists (as a sub-race of humans) try to understand everything that they can.
2. Scientists try to get the rest of the humans to understand before the scientists get lynched/executed/burned at stake/etc.


The two current futures that we have been shown can be easily accounted for by these:

The Pinehearst facilities were seen as scientists that had brought about a formula that could give people special abilities and were working on more all the time. They used this "research" excuse to hunt down specials who interfered with them as "dangerous escaped research subjects" so they could be seen as still working for the public good and have good PR.

The other future, where Peter blew up in NY, was not at the same stage that the Pinehearst future was...YET. It could have possibly gotten there but not without a LOT of help. And where would that help have come from? The Company.