Keep in mind that there is also a 6 second cooldown on Stealth. So If you were to ambush efc, you have to wait 6 seconds before you can use stealth again, even if you use shadowmeld. So you would either have to use ambush then shadowmeld, and wait for the cooldown to end while hoping no one hits you, which is highly unlikely in a premade situation, or run off a little shadowmeld and then stealth and go back. Whichever the case, chances are that efc has been healed by one of his healers by the time you can get a 2nd ambush off.
I feel like shadowmeld is more useful for survivability and when you are 1v1 vs an efc that can't heal. If this is the case, doing shadowmeld stealth then 2nd ambush will work.
Also, especially for a premade situation, I feel like being subterfuge would help when ninjaing flag returns and these are big. Makes me think of Nuremberg from Machine Gun Clicks in that premade video. You'll know who their fc is and it isn't uncommon for someone besides the fc to grab flag and pass to fc. I feel like the extra 3 in stealth would let you play more aggresively when going for flag return ninjas. Can't be sure about this, since I play mage a lot more than rogue, but Saxx, you play subterfuge rogue a lot and get ninjas all the time, wondering if you have noticed subterfuge being helpful when ninjaing flag returns. Do you think it helps for this?