I have made some updates due to recent interviews and articles posted.
1. Adam Warlock
Adam Warlock is the clear favorite to be Peter Quill's father. The MCU has given us clues since we have seen his cocoon and he is very important in the comic book universe during the Infinity Gauntlet. Why Peter's father? Quill was able to hold an infinity stone without exploding immediately because we know he is part human and something else. During GOTG, they reference his father as an "angel" and being of ancient specics Nova Prime hasn't seen in a long time.Adam needs to be introduced sooner rather than later so he can help Earth's Mightiest defeat Thanos in the Infinity Wars. Actors I would like to see as Adam Warlock: Nikolaj Coster-Waldau or Luke Bracey
I am a HUGE Nova fan so personally I would love to him in GOTG2. James Gunn has hinted at not having Nova in GOTG2 but that doesn't mean he still couldn't be Peter's father. Gunn did state however, Peter's father would be someone we don't expect. There is a connection based off of Nova Prime involvement and Rhomann Dey's appearance in GOTG. Richard Rider could have gone back to Earth to find his own past and then had relations with Meredith Quill. Actors I would like to see as Nova (though both unlikely due to contract sizes) : Matthew McConaughey or Jude Law
3. The Collector
Why not? He loves to collect things, why not get his son back. Yondu was sent to capture Peter and bring him to someone. The Collector has been know to hire parties to retrieve things he wants. Half of Peter's genetics weren't recognizable. Side question, who was trying to buy the infinity stone? Let's answer that late in another post. No reason to tell who'd I'd like to be The Collector since we already have one!
Honorable Option: RED SKULL!
How you ask? Well, last time we saw Red Skull he was heading into outer space. How do we know he didn't make it back to earth? Skull has similar attributes as Captain America, maybe thats how Star-Lord was able to hold on to the infinity stone because he was regenerating as fast as he could.