I'm going to have to disagree here. Zero to hero would work in Mass Effect, it's just that writers can't think outside the box. Maybe you're not a soldier at all? Maybe you got picked up by the military ship after being caught smuggling. En route to Space Prison (or whatever) the ship gets attacked by...space pirates? and the commander and half the crew dies. You prove yourself capable in fending off the "Take no prisoners" pirates and in doing so, earn the trust of the remaining crew and basically become the new de facto commander.
Is it a bit of a stretch? Yes. But that's just one of many examples. And besides, you're entering a new freaking galaxy. I'm sure the usual rules fall out the air lock at that point. The only reasonable or logical excuse to not have Zero to hero is budget in my opinion. Because it would take a lot of time and money to progress through that kind of plot without going over-budget or something.
That wouldn't work for me, because I still think it would be quite a stretch that the smuggler is given command of a military vessel just because they helped fend off some pirates. The smuggler would still be an outsider, with no knowledge of the inner workings of that organization, without having advanced up its chain of command, and with no knowledge of that organization's rules & regs or tactical doctrine, and even if he/she knew how to fly a ship, would still likely be unfamiliar with the capabilities and technical details of the ship he/she would now be commanding.
There would also be the issue of the warship being government rather than private property, with its commanders appointed by a central headquarters someplace, and with military organizations having regs that determine who takes command in the event of casualties among commanders. In that scenario it should always be the next highest ranking officer among the crew assuming command, not some Smuggler who was brought on board as a prisoner.
To use a real world comparison, it would be sort of like the captain of an Alaskan crab-fishing boat taking command of an Arleigh Burke class guided missile destroyer. He might be a sailor, but he'd be completely out of his depth.
I favor the protagonist having had a career prior to the player stepping into their boots even if their background is civilian, for similar reasons. A new hire fresh from college would probably be lucky if Baria Frontiers trusted him/her to run the copier machine unsupervised, let alone command a space ship that likely costs the Mass Effect equivalent of billions of dollars.
The same should also be true for less organized folks who might be flying space ships, like pirates. Pirates probably aren't going to elect a newly liberated slave as their captain, if that slave has no prior experience as a pirate and knows next to nothing about operating space craft, interstellar navigation, the shipping lanes, which ports to visit and which to avoid, the capabilities of his/her own ship or those of warships patrolling the shipping lanes, ect, ect. It would be far more realistic for the slave the pirates freed to be handed an assault rifle with the instructions to do as they're told and not touch anything.
Having said all the above...I also realize that everyone has different preferences for what they're willing to suspend disbelief on, but the nobody who immediately gets thrust into a position of importance without a resume to recommend it, strains mine beyond the breaking point in any setting where it can't be hand-waived by magic.