After actually reading the whole thread, a few points: *WALL OF TEXT INCOMING*
1 - The plot holes ("pulling crap") are actually explained. Saren didn't destroy the beacon, it was damaged and using it caused it to malfunction. He had the other one because its signal was interfered with and only about half the message was transfered, that is why Liara doesn't piece it together until you go to Virmire for the other beacon and after going to Feros and getting the Cipher. Saren was killed by a fraction of the Citadel fleet, granted that fraction did have the Destiny Ascension, they were still caught off guard.
As for the holes in Mass Effect 2: The Collector Base did have security; the Omega 4 Relay. The Omega 4 Relay would basically destroy any ship without the IFF. That was the whole reason that you went to the Derelict Reaper in the first place.
2 - All we have seen is the Reapers landing on Earth. Earth is a big planet and even though Reapers are huge, they are still dwarfed by the size of a planet. And we were never explicitly told how long the Reapers spent going from planet to planet and abducting/slaughtering the population. It might take them a whole week to go from city to city, country to country, continent to continent and enslave or kill everyone. Plus they also mined the planets for their resources, so it might take several days for that. And I imagine that they only sent a small group of Reapers to each planet considering how many are in our solar system, they would have to spread out very thin in order to prevent the survivors from banding together into some sort of mega fleet.
3 - Multiplayer would suck because of a couple things: Who is the co-op player? What would you do during conversations? Do you have people that wouldn't interrupt the conversations with chatter? How would they handle Biotic Powers online if it is competitive? What would they do that would separate themselves from the other online shooters? AC:Brotherhood had a really unique multiplayer that has the potential to be continually played for a long time, but how would yet another TPS fair, especially when Gears 3 will be out by then?
4 - By focusing resources onto MP, they'd be taking them away from SP. I don't just mean development time, I know there were job listings for a MP team so if this is indeed the case, the two teams are working separately, but disc space. Especially taking into account that they have to incorporate the choices from BOTH games, as well as a new story and levels and everything. They would probably have 2-3 discs for the SP and then another for MP itself.
5 - The RPG elements weren't removed, they were streamlined, which means, "hidden carefully." You still have choice of weapons, armor, upgrades, etc. they just aren't in a clumsy inventory system. I admit I don't like that you have to go all the way back to the Normandy to change weapons and armor in the hubs. I wish they had Armor Lockers and Weapon Lockers by the vendors that sell them just like how there is a weapon locker a little bit ahead from new weapon pick ups in the actual levels.
It was just made more practical. Rather than a simple and retarded system of listing damage resistance and shields or damage, they list stuff like, "Bonus to Weapon Accuracy" and "Burst Fire" to the weapon and armor descriptions. Rather than just, "which one does more damage?" it became, "This one does more damage, but fires slower." or "This one is burst fire, which makes it accurate, but slow rate of fire and poor up close."
6 - You can have everyone live if you meet these three requirements, (1) upgrade the Normandy's shields, armor and weapons, (2) complete everyone's loyalty mission *successfully and keep them loyal during the arguments* and (3) assign the right people to the right jobs.
Also, if Shepard dies, that save file can't be imported into Mass Effect 3. There is no alteration of save files that has been officially announced. By the time the game comes out, this may not be true anymore, but as of now if you die in Mass Effect 2, that save file doesn't appear for import.
7 - Considering every level of every game should logically conclude with you failing and dying because, statistically speaking, you are way too outnumbered in every level of every game. So saying that you should logically fail at the end of Mass Effect 3 doesn't exactly mean shit.
Although, I imagine one of the endings (or maybe even more) result in the destruction of Earth, the failure of all sentient life, and/or the death of Shepard.