So... basically... Shepad is rubbish?
Actually - if Shepard goes along with (after all we've seen previously) the frankly dubiuous spiel at the end... then... yeah. Shepherd IS rubbsih. More naive than... well I can't thin of an exmaple? Someone who thinks "heartbleed" isn't a big deal?
Is Aria or Omega rubbish compared to the Citadel or Council? Even it proves itself more helpful in the story during wartime?
Is the Krogan rubbish compared to the Turians or Salarians? Even as they saved the galaxy from the Rachni and helped save it from the Reapers?
Is the Alliance rubbish compared to Cerberus (remember that Cerberus is canon that it guided humanity the last decades)? Even as it built the Crucible?
Are the Quarians rubbish compared to the Geth? Even as it was a Quarian that even caused the fight against Saren to begin with?
Sure, the have less power and control over what happens, but sometimes they're... exactly what a problem needs... a little chaos to shake things up.
"I don't need luck, I have ammo!"
But yes, in my opinion, the next Mass Effect protagonist will have quite a bit more 'power' than Shepard did, even towards his end.
A Shepard that picked Control or Synth did betray his allies though. He..just did. He went against all intentions he was placed with. Pick Control and you establish your independence from what Commander Shepard was 'supposed' to be. Pick Synthesis and you outright 'side' with the enemy.
But I don't think he was rubbish. Ever.