Well the threat factor of Luffy to the World Government has raised considerably after the two year time skip…Lets take a look at the facts
First there was the return to Shabaody, and the fact that Sentomaru witnessed first hand Luffy's new found power of being able to control Haki. The World Government knew that Luffy possessed CoC haki, but that he was unable to control, or even aware it himself. The second Akainu saw Luffy use CoC, he made it his sole mission during the war to kill Luffy, before he could develop even further. If Sentomaru brings back word that he witnessed Luffy using any form of Haki, Akainu is going to realize just exactly what it is Luffy has been up to the last two years, and that now Luffy could actively control the very thing Akainu wanted to make sure didn't happen in the first place.
Second there is Luffy's declaration of War against Big Mom. For some reason every little thing the Straw Hats do, end up on the radar of the World Government, and if they have gained knowledge that Luffy has declared war on one of the Yonko's, it will raise his threat level even more.
Third there's the events on Punk Hazard. We all saw what happened last time Luffy did Smoker's job for him. Luffy got all the blame, and Smoker got all the credit (much to Smokers displeasure) Someone is going to have the take the blame for experiments done on the children, the production of SAD and weapons of Mass Destruction, and since Fujitora cleared Caesar of all charges because of being one of Doflamingo's subordinates, then sadly that blame is going to fall on the Straw Hat/Law alliance. Once again making them an even bigger threat level.
Finally we have the Luffy/Law alliance, and the fact that Law has now been stripped of his schichibukai title. The government will see an alliance between two supernovas as a huge threat to them, especially, if/ when they take down Doflamingo. Now that law is no longer a Shichibukai, his bounty of 440,000,000 is once again active, and he himself will be getting a bounty increase, and I believe Luffy's bounty will once again become higher then Laws. I see Law getting a 500,000,000 bounty with Luffy's bounty at least 50,000,000 higher.
Coincidentally Kid, Hawkins, and Apoo will all get bounty increases also because of their alliance as well.