Thus losing utility. Where will those ships with civilians be? Separated from heavy and patrol fleet and easy prey for pirates and other enemies?
Their plan was sound. In 17 days they liberated 4 star systems. Without reaper intervention by day 20 they would probably be done with the Geth, and able to assist with the war against reapers
Not really. It means that you put them in key locations in the formations where noncombatants will be considerably less of an issue. Like to the point that you don't even need to bring it up. Noncombatants aren't just limited to civilians. It's also key personnel such as admirals, medics, engineers... Or essentially anyone without combat experience-- people that can assist in the war effort but aren't necessarily soldiers. Think about someone like say, the primarch, he was combatant at first, but then when he became the primarch through circumstances, he was no longer permitted to fight. By having better diversity of the ships, this would have allowed for more aggressive combat without needing to worry about key people or civilians actually being put into any real dangers. Not to mention, putting civilians in other ships would not mean putting them in ships that offer no lines of self-defense and sending them to the darkest corner of the galaxy.
And the timing is my issue. Why for instance, couldn't it have been done in the time frame between ME2 and ME3? There was at least six months? That said, this conversation really isn't needed for the topic at hand and is it's own thing.
As for the Geth, I don't see how from a non-metagame perspective you could side with them. Even assuming they had sentience as a hivemind, there are problems with siding with them over the Quarians. In ME1, they were gung-ho about killing you. Sure, legion says that those were the heretics, but how can I believe that? Because it says so? I haven't analyzed any of the code to even know how this could have happened, so I'm not sure I believe it. For all I know, in the 200-300 years the Geth were in the veil, they learned the benefits of lying and played me like a card. Even assuming that I DO believe legion, the decision you can make at the end of the mission solidifies that I wouldn't want them as an ally. The fact that I can just rewrite them and make them believe what I want to be right is bad. It means that anyone else can do that. The last thing I want is a Geth going ballistic and shooting me in the back because someone mucked with its "friend or foe" process. For cripes sake, Tali can just hack ONE and make it go crazy with the wave of her hand, heck, Sheperd might be able to do that him/herself! Do you really want that as an ally? And even if you bring up the Reaper code can defend them from being hacked like that, here's the thing, it's reaper code. I know even less about it than I do the coding of the Geth themselves. Organic reprogramming is already a thing via indoctrination, what's to say that a synthetic can't be programmed either? For all I know, the reaper code could have a dormant virus within it to infect the system after it's been dormant for a couple of days or so and activates sending the synthetic into a crazed frenzy.
At most I can see a reasonable argument for pacifying both the Quarians and the Geth, or destroying them. I really can't see how a person could even think the Geth should be preserved over the Quarians from a sheer "I want to win the war in the safest possible way." I can only see a preference if you just don't like Quarians. Which even if I did, I see no reason to eliminate an entire race.