Indoctrinating the exhausted and crippled soldier with damaged armor and armed only with a pistol, who has no idea where your "self destruct button" even is - assuming that such a thing even exists - or how to activate it, whose entire plan for beating you has already played out to its end and exhausted 99% (or whatever the fraction actually is) of the resources he could possibly draw on? Yes, I would call that nearly worthless.
Suppose Shepard staggers off, trying to find a way to activate the Crucible. He doesn't know what he's looking for, or where to find it, or what to do with it. 5 minutes later, the Reapers have damaged the Crucible enough that it no longer matters.
Suppose Shepard miraculously escapes somehow. The Systems Alliance Navy is gone. The Turian fleets are gone. The Asari fleets are gone. The Salarian fleets are gone or in hiding. The Geth are destroyed. The Quarian Migrant Fleet is gone. The Krogan are greatly reduced, and they're specialized as ground troops anyway. Even the Batarian fleet is gone. What's he going to do, rally the Hanar to oppose you?
Suppose you do Indoctrinate Shepard and send him out as your agent. The Systems Alliance Navy is gone. The... I won't bother repeating the list. What's he going to do, sabotage the Hanar forces? Why bother?
Having both Control and Destroy available was also limited by War Assets, and if you didn't have enough then which one you got was decided by whether you salvaged or destroyed the Collector Base in ME2. Paragon/Renegade did not affect it, aside from which one each option for the Collector Base corresponds to.
Paragon/Renegade does affect some of the ending cutscene stuff, though. The detail that I know of offhand is the attitude of the phrasing Ascended Shepard uses in narrating the Control ending.