Right, but I meant BEFORE the REVERIE.
What was stopping them when they had the full power of the warlords, and Garp and 3 admirals?
Pre-TS:
Multiple things, the issue of taking down an emperor on it's own is not an issue for them per say in a vacuum. However, the issue arises when you talk about it being in the One Piece world itself.
When they took down Whitebeard, did they have any issue? Nope. Hell Whitebeard pirates would've been slaughtered to the last man, without a single major marine dying (no VA or Admiral would've died, not even relevant Captains like Tashigi). However, they did have issues after Whitebeard got taken down, to a point where they didn't even have any relevant Marines stationed at Marine HQ. Even in East Blue things were getting riled up with Luffy's village being attacked by pirates and so on.
This was so bad to a point that they didn't even have the forces available to go after Whitebeard's territories, which allowed the likes of Blackbeard to gain them.
Now imagine taking down two Yonko, the amount of shit storm it would cause around the world would've left the Marines the way they were after WB got taken down, completely defenseless. Because remember it's not like they can instant teleport everywhere, this is still taking days to weeks to go from Island to Island, enough time for pirates to escape and go do damage somewhere else, so on and so forth. (Travel time is a huge restriction, when you have to monitor the entire world).
#2. The Gorosei. Marines can't take on the Yonko even if they wanted to without getting O.K from the the Gorosei. The Gorosei who want to keep this charade up, where the Yonko eliminate the weaker pirates, instead of them having to do it themselves. Simply look at how many pirates the Yonko have taken care of. Why would the Gorosei want to disrupt that and make it more chaotic? They don't have any reason to. Sure they want to prevent people from knowing about the History and becoming the Pirate King. They know the Yonko aren't a threat to a point, where they're making deals with the Yonko.
-> Using Doflamingo to make deals with Kaido, which now got taken over by the CP0
-> Literally having a meeting with another Yonko in Shanks. What was their attitude to a Yonko being in there with them?? Casual, continuing to read their newspapers. Instead it was the Yonko who was thanking them for their time, unlike his Marineford self where he came in cocky saying he arrived to end the war.
They don't have the numbers to subjugate Yonko territories completely while also keeping their own territories safe throughout the entire world.
Post-TS:
This is where you could possibly question that Marines have the power to do all of that, but haven't they done so? They're far stronger than they have ever been in their history, they're more determined than ever before... They two new powerhouses, GB & PT. But issue post-TS isn't about power, it's about time and availability.
It's been less than 2 years since the Marines switched leadership, and did their military draft (probably a year or so at best since the Draft). So it's not like they had fuck ton of time to think about invading Kaido & Big Mom. And by the time they're all set, it was time for reverie, meaning they can't make major moves that'd disrupt the seas putting the royals of the world at danger, considering they're dedicating multiple ships to their safety already and we're already seen people trying to attack the royals.
Then after the reverie we have multiple things taking place. With only option left being the SSG.