I'm gunna go all out here and try and speculate how I see Phase 2 shaping up. It gets a little lengthy and I'm really bored right now haha, but it's a really good read. I think it's pretty interesting and I'd love to speculate with you guys and spitball different ideas. Let's have some fun!
Notice: I have no sources and I am entirely speculating here.
Notice 2: The person I refer to as 'LokiD' is a member on the SHH forums who also has interesting ideas on Phase two that I've adapted into my layout as well. (He claims to have a source for his info, but mine is purely fun speculation.)
So we know Iron Man 3 is introducing Extermis, which we can pretty safely assume is a recreation of the Super Solid Serum. This ties in together smoothly in the MCU w/ Red Skull/Blonsky being failed attempts and Cap being the only real one. It could also possibly tie in with Bucky Barnes/Winter Solider getting the Infinity Formula which could be another variation of the Serum (not sure what the Infinity Formula really is though)
Lets also assume that an early A.I. version of Ultron is in play, possibly something like (U.L.T.R.O.N.) on a computer screen as a defensive system or computer system that AIM has gotten a hold of in order to combat with Tony's J.A.R.V.I.S. system. We can assume this was created by Pym either in the present day timeline of event of Phase 1 or early Phase 2 (possibly in the year between Avengers and IM3).. I still don't think they're going to be adapting the Past/Present storyline of Ant-Man that's been specualted at however many years ago, keeping it more grounded in the present MCU makes more sense to me.
So from the start of Phase 2 in IM3 we can possibly see a future route of Ultron in play (in some small capacity, maybe setting up a long run story line for Avengers3 and to drum up some noise for Ant-Man, which is probably going to be Marvel's biggest chance movie along with GotG.) And on the topic of Guardians of the Galaxy, if reports of Tony getting an S.O.S. from deep space and wanting to investigate are true, that's also being set up in this movie as well. Both are very smart moves by Marvel in my opinion because those are the two movies they are probably most concerned about so setting them up in some capacity in Iron Man 3 (which the most people are going to see) is a really good move I think.
Moving onto Thor I'm not really sure how or what they are going to put in there to connect with Avengers 2, possible GotG S.O.S. of some sort to Thor or Odin could make some sense to me (also since I've read Thor and Tony are called to the aid of the Guardians, probably after they face their movies threat i.e. Thanos I would guess.) I like the Maleketh/Kurse storyline they're doing, and from the set pics we've seen where Jane is holding that strange device it could possibly play into some sort of storyline that leads us in a general direction (I don't even know to speculate how or what it would be though).
Onto Cap2 I'm going to run w/ what LokiD just alluded to with the revelation that Zola and Zemo with a re-created HYDRA are possibly the ones being present day AIM (HYDRA reincarnated) This completes full circle ties with IM3 storyline of Extremis that let's say Zola had a hand in creating the virus while also creating the Infinity Formula used for Bucky, and other side projects turning Simon Williams into the Living Laser. (Not too harsh of a stretch considering he's had decades of time since Cap1 ended to work on all these projects) They are also working with this new AI system (early Ultron prototype) to try and essentially do what Tony did with the H.A.P.P.y armor transferring a persons brainwaves to a sentient armor. So with what 'Loki' said, over the course of this movie Simon Williams turns good and now we have his brain patterns with Starks knowledge of how to transfer brainwaves inching closer to a full fledged Ultron system.
Now I think, and really hope won't we see a robot Ultron until Ant-Man where Pym working with Starks notes and his own knowledge creates Ultron after the events of Avengers 2 in order to prevent another catastrophe like this from happening again.
On to Guardians of the Galaxy, we'll get an orgin story of sorts introducing Starlord and his background (possibly he knows people already in our current MCU) along with the rest of the gang. Now I don't know much about the GotG comics, but I assume they and Nova(he's gotta be in there) will be facing off against Thanos and ultimately lose to where they retreat and regroup and send out the S.O.S. that reaches Stark and Thor who investigate with them. They tell Tony and Thor that Thanos is heading their way and they need to prepare.
So Avengers 2 we have Thanos coming to attack in the imminent future, and I'm going to also assume that the Master of Evil are going to pop up in some form in this movie too. So lets say one big mastermind of the baddies we've seen so far groups this team together, (maybe Leader which could be the direct reason Hulk gets back involved with the team, or someone else like The Other [doubtful] or Red Skull or even Loki [Hope not] pull this team together) So now with the knowledge that Thanos is coming the Avengers are faced with the Masters of Evil problem as well. So lets say act 1 we see both teams coming together, Avengers get a few new members and MoE are forming as well. Lets take 1 villain from each persons movies. (Mandy, Zemo, Maleketh, Blonsky, with a main boss calling the shots (Leader, Red Skull). Act 2 comes around and each character takes out their villain one by one, and as the battles are coming to an end Thanos arrives act 3.. they give it everything they've got and put up a minimal fight effort and then when all is lost back up comes in the form of GotG and Nova and the tables then turn and Thanos is defeated. (now I know that is a stretch for this movie and you've got to put some dialog story crap in there somewhere but I would enjoy the hell out of this film haha.)
Throw in other AIM/HYDRA related storylines over the course of the films since I think they will play a big role in this Phase and I think we've got a pretty cool Phase 2.
So after Thanos is defeated or forced to back out from being overpowered or whatever, we start off Phase 3 with Ant-Man who then creates Ultron as some sort of major defense alert system that at the end of Ant-Man turns on him. Not going to speculate past that since we don't even know what movies to expect.
So if you stayed with me here, how do you guys feel about that. where could we add or subtract. What storylines could be put in play in place of those that I suggested. Lets get a fun discussion going.
Leave your feedback in the comments please!! :)