ME3 will have plot holes.. it's inevitable. But as long as they tie everything up well enough, and present it as if it all makes perfect sense like in ME2.. I'll be happy.
I like to think of it in terms of all the fancy science talk in Star Trek that you don't understand... but you have to buy into it anyway for the sake of the story.. because it's science fiction and you need to just accept it... so go with it.
****BEGIN SPOILERS****
Mass Effect 2 opens with the death of Commander Shepard. This is an inept way to begin a story. Shepard dies, there's a cutscene, and he's alive again. Begin tutorial. If you do kill a character in the opening scene, then you'd expect the game to be that character working through the experience and growing as a human being. But Shepard is up and capping robots in seconds, and the whole "I was dead" thing has no impact on him as a character.
Opinion... to each his own. But I actually liked this element of ME2 for numerous reasons:
1. It allows for an excuse to change something about your existing Shepard (god knows why you'd want to.. but it's convenient).
2. I think it helps elevate Shepard above his Spectre status. He's officially recognized as KIA, his ship is gone, and his ties to the Alliance and Counsel are severed for 2 years. When he returns, he's like a ghost and really doesn't answer to anyone (except the whole Cerberus railroading, blah blah). And he's got cybernetic enhancements now... maybe that will lead to something later.. maybe not.
3. The first teaser trailer with him being KIA really fucked with people's minds.
4. It allowed for one of the best opening scenes in recent years.
5. If Shepard had died at the end of ME... bringing him back at the beginning of ME2 would have felt like a copout... At least with doing it within the same game, it didn't feel like they chose to make a sequel after the fact.
6. Though bringing him back may have seemed too easy... they at least tried to make it seem like an incredibly difficult and costly procedure... so the argument of "constantly cloning Shepard if he dies" never really becomes an issue.
Again... this is just my opinion... you made some good points, but most of the plot holes you named didn't really bother me because they just presented it so well.