I've been reading the online graphic novel... which states that Linderman and Petrelli, Sr. served in Vietnam together, and shows little Nathan playing with his airplane during Linderman's first visit.
So, nope; Linderman, you are not the father...
However, if Linderman is the father of Meredith (the pyrotechnic), then he could be Claire's grandfather. I've been joking with Bryan for months about Linderman's Mendelian tendencies... that maybe he's secretly breeding evolved humans to take over the world. What are the odds that he purposefully paired Meredith with Nathan, just like Niki/Jessica was paired with him? Isn't it odd that both DL and Niki have powers? That they produced Micah?
I like the way you think, regarding Hiros... I kept wondering if there was a paradox that would rip the fabric of the space-time continuum if both Hiros met.
My personal theory is that in Five Years Gone, we find out that Sylar killed Ted and Candace, thus gaining the abilities of nuclear power and of illusion. Sylar then impersonated Peter in order to get close enough to kill Claire. Peter's visions of fighting himself, of causing the explosion, might actually be about Sylar in disguise. If Sylar frames Peter for her death and the explosion, then a newly-elected Nathan would be forced to hunt down his own brother.
To mess with your minds, I'll go one further...
What if Sylar later impersonates Nathan and takes over his political career? What a tempting target Nathan Petrelli would be! *yum*