Rastrelly said:
Okay, lots to get to.
1)So, the Conduit. Now, as I understand it, no one knew what the Conduit was. It probably wasn't until Saren reached Ilos that even he or Sovereign became aware that the Conduit was merely a mass relay leading to the Citadel. So, if you are Sovereign, and your many-million-year old plan has suddenly gone awry when your signal to the keepers doesn't work, and you know it is because of some prothean technology called the Conduit, what do you do? Do you immediately bum-rush the Citadel in the hopes that when you get there you can figure out what went wrong? Or, as an ageless space cthulu, do you take your time in figuring out what the Conduit is and what the protheans might have done to your signal, to make sure that the next time you try it actually works out? Sovereign wasn't going to gamble on this, he needed to get it right. In fact, probably the only reason he moved when he did is because Shepard had begun taking his plans apart, and he needed to act fast before the whole galaxy knew what he was about.
This is why he has Saren collecting beacons, trying to find info on the Conduit and what it did. Saren only came to the conclusion that it was on Ilos at the same time Shepard did, since he also had to go to Eden Prime to check out what this newly discovered beacon might say about the Conduit, to Noveria to get the Mu relay location from the Rachni, and to Feros to get the Cipher from the Thorian. Virmire is a bit harder to explain, but I imagine that he and Sovereign thought the Citadel would be a lot easier to secure if they had a few hundred krogan to go in and wipe out C-Sec forces. Again, remember that Sovereign has, literally, all the time in the world. He can wait centuries if need be to lay his plans, as long as no one finds him out. Which Shepard finally did.
2)So, next point. The Omega 4 relay. No. Listen to yourself. The Council WOULD NOT send a military force to Omega. If they had, that would constitute an ACTUAL plot hole, being a complete contradiction to their statements in the previous game that they would not send any fleet into the Attican Traverse. The Terminus systems, where the Omega relay resides, is a fractured and unstable region, but they fear the combined power of the various governments and organizations there if they had reason to unite and fight a perceived invasion from Citadel Space.
Whatever threat the collectors pose, it is not enough to start a galactic-scale war. The collectors, as Anderson himself says, "have always been considered a fringe threat." They only deal in the Terminus systems, and they only ever appear rarely. No sane Councillor would even propose a military expedition to the Omega 4 relay.
As far as a scientific research station, that's still debatable. Quite possibly they did have one there at one point. All they found, apparently, was that the relay only let collector ships through, and anyone trying to follow them never returned. This is not a major concern, it just means you have to tell everyone not to go through the relay and leave it at that. Anyone foolish enough not to heed the warning only got what they were asking for. It's a scientific curiosity, but not a top-priority one. There are plenty of other forbidden relays leading who-knows-where for them to wonder about, including ones that are not all the way out in dangerous and lawless space.
3)Okay, it is hard to defend some of that. I will concede that it makes no sense to build the Crucible that fast. It is unfamiliar technology, it is nearly the size of the Citadel itself, and the timeframe probably wouldn't allow for that. As the game goes on you do continue to pool resources into the project, until near the end you have most of what remains of the galactic community building the thing. And the game actually place over several months, not weeks. But still, it's a lot to buy that they could decode the plans, understand the concepts, and then construct it that quickly.
Also, yes, there is little sense in the reapers allowing themselves to be bogged down in ground battles. You do eventually (at the end) find out that they are concerned with preserving as much of a civilization as possible, and that may be why they would take such a tactic. But then you remember that all over the previous games you find evidence on abandoned planets that the reapers have no issues with completely obliterating a population from orbit. So yeah, it's damn unlikely that they wouldn't just do that to all these pesky organic armies, especially since they don't have the advantage they have always had of starting the war by killing all the galactic leaders and taking control of the mass relay network.
But the thing is, since it's a third person shooter, they needed to have the reapers do what they did or else Mass Effect suddenly becomes a space combat game. Really, the problem is the way they had set up the reapers in the previous games. It was a corner they had no way out of other than to just ignore the issue.
And the reason they began with the reaper invasion instead of your idea....It's more exciting this way. The game gets to be about the horrors of war. Also, since you've spent the first two games essentially doing just what you describe, preparing for the reaper invasion, it would get repetitive the third time around.