1) Harbinger ain't sending anyone to stop you, you are stopping THEM. What do Reapers do? They HAAAAARVEEEEST, whether directly or with the use of previously-harvested minions like the Collectors. And you're in their way. So yeah, I'm glad we got to play that chapter.
It's like the calm before the storm. You think you're safe, but the black storm clouds are gathering on the horizon. The Reaper threat is still there, just veiled.
And in ME3 when they've finally arrived, well, there's alot more to worry about than just Harbinger, how about 1000s of his buddies?? Yeah they could've included him a tad more, but it's hardly a heavy loss.
2) The starbrat's eyes are brown, which is a glaring indicator of what he's full of

, so I wouldn't pay too much attention to his "logic" if I were you. He clearly don't know ****.
3) Cerberus was indeed morally grey, because the Illusive Man wanted them that way, he's the one in charge. It's clearly obvious though, during the later timeline of ME2 that he was slowly becoming indoctrinated. Probably from the pieces of Sovereign they recovered. So as his "views" change, so does the rest of Cerberus. By the beginning of ME3 he's already gone off his rocker, which is why Cerberus becomes a threat to those who oppose the Reapers.
He's also mixed with a lil madness so he goes even further off the deep end, which ticks off the Reapers eventually.
4) You're looking at specific points, whereas you should consider the bigger picture more. There's more to do in the universe than hang around Shepard 24/7. They were only recruited specifically for the suicide mission. Whereas, say, Kaidan was already there from the get-go. Ashley was closely behind Kaidan.
Garrus was sick n tired of all the red tape, which is why he joined Shepard. Liara is overly needy, so she came along too

. Wrex, not sure why he came along actually, aside from the Fist thing. Tali had vital evidence against Saren, that's why she came along, and she was once again encountered by chance on Freedom's Progress, which paved the way for her to return onto the Normandy.
The rest of em had their own personal agendas to pursue, and most of them made it clear they wouldn't be sticking around after the suicide mission anyway. And not everything has to always link to something in the previous game, I prefer trying new things too.
So yeah, depends on your point of view. They couldn't have brought in the Reapers at full force in the second game, otherwise there wouldn't be much to do in ME3. The war would've been over in ME2 and the galaxy would either be a smoking ruin or a war-ravaged wasteland. There's hardly any viable setting for the game in such an environment. I mean, this ain't Fallout 3/New Vegas, ya know?
The war against the Reapers would have ALWAYS happened in the third chapter. The Collector diversion was great, and they're creepy as hell.