I would quote all the arguments I want to refute, but it's easier not to, so...
@Everyone who says WB was the main target: Why? Why would the WG, after stabilizing their reign over almost all of the world, go after WB now? Why? He's old, and he's going to die eventually; most of the people around the world don't even fear WB anymore (except those who live near grand line and the new world). WB's just a legend now; he cannot do any harm, nor would he unless provoked. So then why go after WB? Dragon is the only one fighting the WG head on, not WB. Going after Ace for WB would be like saying going after Luffy for Dragon. However, the WG didn't go after Luffy when his father is the greatest terrorist in OP world; yet the WG goes after Ace who's "father" is and old, dying man?
Doesn't really make sense, does it? Going after WB would inspire a new era, just like when they went after Roger - and that seems to be the last thing anyone in the WG wants right now. So, it raises the question; Why? Why would the WG willingly fight WB after all this time? Even while showing such hesitation and having the knowledge that facing WB could potentially wipe the marines and shichibukai out (thus destorying the WG), why would they do it? It's not like one day, Sengoku and the Goryusei were like
"Hey we're bored right? fighting dragon is boring... lets go face WB. It'll be like a match of starcraft; our zerg rush vs their protoss fleet. Any one wanna make a bet of who wins?"
Seriously, it doesn't make any sense. The only reason they would be willing to fight WB would be if they had NO OTHER OPTION. The significance of this battle isn't the start of a new era, it's the fear the WG still retains from Roger. They were that fucking scared of another Roger appearing that they would face WB who was protecting Ace. If they wanted WB, they would've just zerg rushed him years ago. But no, they didn't, because they had no reason to. With Roger dead, WB would have no one to battle on the seas, fights on the seas would decrease, less civilian casualties, the WG gets the closest thing to peace they could possibly obtain.
BUT THEN THEY FOUND OUT ACE IS ROGER'S SON AND ALL HELL BROKE LOOSE.
"FUCK PEACE, WE NEED TO KILL ACE. WE NEED TO END ROGER'S BLOOD LINE."
So they promoted someone who they knew Ace was after (BB), and used him to catch Ace (thus, indirectly, catching Ace themselves). Then they broadcast his death just like they did Roger's, so that the entire world can see their triumph. They set a concrete time, because that's how all major public executions are held (Saddam Hussein any one?). Thus, the WG did what ever they could to kill Ace at that alotted time, so that they could end Roger's reign over them;
-They brought their entire force to stall the battle with WB
-They started a rumor saying that they would kill Ace ahead of time to disrupt WB's tactics, as it would lead him to rush and end up defeated
-Aikinu (or w/e) used squid to attack WB so that they could stall longer
-The Kuma Brigade was used take out all the small fry that would get in the WG's way; thus eliminating majority of WB's offensive power
-They raise the gates to trap WB so that he wouldn't be able to get to Ace
-Then they kill Ace and WB (since they had to kill the latter once they started a battle with him)
Thus, again, the main target was, and always will be, Ace - or rather, it was Roger. Come to think of it, it was always Roger. Roger's blood. Roger's son. Roger's legacy. To defeat the Pirate King once and for all, the WG would sacrifice everything. In the end, Ace and WB were insignificant. It was really just Roger's Era vs The World Government.
And the World Government lost. They lost to Roger's will. In the end, all they accomplished was the death of a lot of insignificant men and women, the death of a yonkou, and their image tarnished forever since they couldn't kill Roger's son.
and so beings the new era...