Here's my opinion on a couple things:
- The person who shot nathan must have been a "good shot" since he was shot right in the chest from quite far away. A lot of company people (including HRG) are good with guns, and probably could have done it. But company people always go with a partner, so HRG could have stayed with his trusty hatian or gotten a new partner who helped him shoot nathan.
- For Angela Petrelli's power and Charles Deveaux, i've found that using peter to discover their powers has given me some great theories. Peter was somehow able to dream the future (he dreams multiple things, including nathan's car accident), and there is always a connection between charles and peter's dreams. Peter probably copied charles's power when he met him, and used it right away. As for Angela Petrelli, I think her power lets her project herself through time and space, kind of like hiro. Peter does this a number of times. One time is at the end of season 1, he appears on the deaveaux roof and speaks to charles, if he was just invisible, charles couldn't see him, but since charles and angela were old pals, he was probably familiar with angela's power and could detect it. Another example is when he just meets adam after his memory comes back and he flashes to the future to see katlyn for a bit, at which point adam "wakes" him up and tells him he was screaming a name for a moment.

