Let's see here...
1. I can agree with to an extent, BUT a plothole isn't made by a gameplay mechanic. At that rate, anyone who has ever died at some point during the game has created plotholes. gameplay=/=plot.
2.Various possibilities, even down to the fact that Wilson is explained to be the traitor, so would it really be so far-fetched that he, I dunno, shot himself to make him look better? Which doesn't even make Shepard look stupid, because when you're in a high stress life or death situation, you aren't always likely to notice the absence of evidence. Other reasons are given by TUS. Also possible, that like several mech's throughout the game, it blew up and there was no body left to be found.
3. Not a plothole. Very plausibly a VI autopilot that knows how to get from location to location, and completely insignificant to the story so does not really merit the addition of Shepard, who would know how the ship was flying, asking about such, nor even merit the scene being extended just so that Jacob or Miranda could say "Ok, autopilot's been set."
4.I live in Illinois, and have to deal with a lot of snow. I've seen it snowing heavily and accumulating when it's in the upper 30s. There is no indication that the temperature is too cold to be eating outside, especially considering I have, and have seen others, sitting around outside as temperatures dip into the teens and 20s. This is your personal opinion, not a plothole.
5. As TUS said, Miranda specifically states that Veetor must have re-assembled the data. It's even very possible that he was hiding and controlling the camera's during the attack, when they are usually cut off. Either way, Miranda's line explains it, considering someone actively piecing together data as things occur is going to have much better luck than someone going days later and trying to do so.
6. TUS explained. Regardless of Shepards background, he's on a Cerberus space station, and is told, "hey, this colony got attacked, why don't you go check it out, and if there's nothing there, you can leave." Shepard isn't going to look at him and say "nope, you just brought me back to life, and I'm on your space station with no feasible route of my own off it, and there's a colony that's been attacked, but I don't like you so I'm just gonna stay here until I think of a way to magically teleport to someone I do." It's not a plothole, because just like the prisoners on Purgatory, if you try to leave, where exactly are you gonna go?
7. Explained quite well if you listen to Liara later. Collector's wanted Shep's body, Shadow Broker had it stolen from him prior to selling it to them and would be interested. Made quite clear in the game that Shepard would fetch a high price.
8. It's called dramatic effect. Once again this stems to gameplay=/=plot/cinematics. If you're going to call this out as a plothole, are the several deaths in many cinematics where it only takes one shot to kill, let's say a Krogan to fully emphasize the point, plotholes? No. They're there to show the real effect of things, gameplay is there to give you a challenge. Regardless if Jack can take down 3 YMIR mechs alone or not, it would absolutely break the game to be able to do so. Is it a plothole that Thane can't kill multiple people before they know he's there? Is it a plothole that Garrus can't be told to get in cover at a bottleneck and have no one get near him? Or that Samara can't absolutely dominate every enemy with biotics? No, because if the characters could fight as well in gameplay as they could in cinematics, there would be no reason for there to be gameplay.
9. Don't see anything that you wrote there that is evidence of the Reapers? Proof of Collector attacks from Freedom's Progress/Horizon, doesn't say anything about Reapers... The DNA simply suggests that the Collectors are modified Protheans, doesn't incline to the Reapers at all. The derelict Reaper only you/Cerberus see before you blow it up to escape, so not sure how that's going to work as evidence since it's, ya know, blown up and crashed into a brown dwarf. Legion's comments mean nothing to them, because they have no reason to believe Legion. If you had been attacked by a group, then they come back and say that it wasn't their fault and the super-weapon wasn't their technology, are you going to believe them or refuse to be lulled into a state of, as far as you know, false security?