Well for starters there is no "correct" options, only choices or consequences. There's no way they're going to make it so that (for the sake of argument) a choice you made on Eden Prime will totally screw you over in ME3 and cause the Reapers to win. Only decisions made in ME3 itself should be able to categorically decide the outcome, anything else is just window dressing.
Indeed we can already see what kind of affect earlier decisions will have based on ME2. For instance, letting the council die in ME1 means you get racist snipes from Turians and a vaguely Orwellian vibe on the Citadel in ME2. The difference between this and if you saved the council is more textural than anything. Sure it was a major decision but it didn't really effect the plot did it?
Most if not all of what you listed will each most likely have their consequences and will most likely effect what the state of the galaxy is by the time the credits role. Still, the "MAJOR" decisions will of course have to be the ones that you can't avoid, like saving Ash or Kaiden, saving the council or letting them die, the rachni queen etc. etc. You can't have an important story element hinge on anything that happens in an optional mission or DLC because some people simply might not have played it.
For example, take the Legion mission; it's not a simple binary decision of destroy or reprogram the heretics. There's a third option in which you can choose not to reactivate Legion and just turn it over to Cerberus for the bounty money. Likewise with the Genophage research, you don't have to do that mission at all. Indeed none of the loyalty missions are compulsory to complete the game so ME3 has to allow for players who chose to do nothing but the bare essentials.
The real question here is what effect your decisions will have and how will they interact? In general terms I think the decisions that have the most effect are the ones that either rally other races and allies against the reapers or divide them. So yes, if you spared the rachni queen, converted the heretics, discouraged the quarians from war and cure the genophage you'll probably get the proverbial cavalry charge that could hypothetically turn a pyrrhic victory into total victory, but not doing so should not necessarily result in defeat.