current? Waller has Checkmate and the Squad. She takes this.
but back when Fury was in charge of shield? hmmm.
Waller is more willing to be ruthless, but Shield definitely has better resources and better tech. We've never seen anything akin to the Psy Ops or to the crazy devices Nick has access to. but Waller has shown herself to be consistenly faster in making tough decisions. Fury takes this when he's in charge of Shield about 7/10.
Current Fury though ends up as just a splatter on...THE WALL.
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considering he's managed to escape capture from SHIELD so far is impressive especially since they're headed by I-Can-Control-Any-Computer-and-look-into-any-cyberspace-crevice Tony Stark. C'mon give the guy some props plus he's got secret access to all sorts of SHIELD secret areas and tech that noone else knows about or can access including Tony. The guy can beat Waller.
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Waller is a stone cold bad-ass though. probably my fourth favorite character in the whole DCU. Waller has checkmate and the resources of the Suicide Squad again. You are right- he has managed to evade capture, but I don't know how easily he could launch an operation to take out Waller from hiding.