Probably because 1) it was thought to be impossible and 2) that would preclude any chance of learning more.
1) Depending on which order you play the game in Shepard can have actually already blown up a Relay before getting that close to even going on the suicide mission. Even if played in what I assume is the correct order a research team had managed to calculate they could be destroyed... were Cerebus with their massive funding (even if stretched by Lazarus) and fingers in many pies (and communications arrays...) not able to do the same?
2) Research and learning more is only presented as a major concern as you prepare to blow the base. Prior to that every mention of learning more about the Collectors was tangent to your central mission... rendering them harmless. Additionally as what we must assume is the paragon ending (seeing as every team mate supports it) includes blowing up the base precluding all future research it appears that learning more is not seen as a major concern.
Like many of these issues it could be dealt with by a few lines of dialogue early on. Very quick example off the top of my head:
Shepard: Couldn't we destroy the Relay?
Illusive Man: Doing so would destroy the entire Omega system, killing everyone there.
Paragon Shepard: That's too heavy a price. We can do it without resorting to such measures.
Neutral Shepard: A heavy price. There must be other options?
Renegade Shepard: Do it. What do we care of the fate of a few thousand against millions?
Illusive Man: The Galaxy would put its entire resources into finding who did this and going after them rather than preparing for the Reapers. We have to think of the bigger picture.
It's the lack of such things that cause the issue.
I see two possibilities. Either they take him about as seriously as we take people predicting the end of the world, or it's all political, and they know but seek to avoid galaxy-wide panic. Just a thought.
1) Shepard, who (especially if played Paragon) has been polite to the Council, consistent about the Reaper threat and seems to be absolutely sane... in addition to all the fallout from Sovereign's attack is several steps above the usual "Doomsday prophets". Every piece of information we've been given indicate they don't believe him... but think he is sincere and are making real attempts to verify (or disprove) his theory... apart from the obvious one
2) If they know then why, in private, don't they agree with him? If they know then why aren't they taking steps under the principle of something else to prepare? Every conversation with the like of Anderson (who is a Council insider at worst) indicates that they simply don't believe him and aren't doing anything and from what I recall of the Galactic News, the only item that would indicate them becoming more prepared is the construction of a few more Turian ships... which it says are to replenish the losses caused by the battle of the Citadel. It takes a remarkable amount of essentially fan-fiction to paint the Council as anything other that beyond incompetent on this issue.
Probably because it's less time-consuming than giving custom weapons to NPCs only encountered on one planet, but that's just a guess. I see your point, but I really fail to see how this damages the plot in any way.
It's one of the many small gap in logic that add up to a greater whole (or hole...). I understand it's minor but it's frustrating... and something that an editor should have caught early on. As long as the logic, plot and setting of a game are internally consistent then it's hard to really fault plot holes... things like this make it inconsistent.
One reason could be that the attack on the Normandy takes place some time after the Citadel attack. If nothing else, he would have known of plans to implement them.
I believe the time-line is somewhere between 3 weeks and a month between the Attack on the Citadel and the original Normandy being destroyed. That seems remarkably little time to roll out a whole new weapons system. In addition, going by the codex entries it was the Geth that developed the thermal clip technology which was later followed (after being originally doubtful) by organic arms manufacturers. Seeing as we see no Geth using thermal clip in ME1 that means that in the 3 weeks to a month between the end of ME1 and start of ME2, the Geth rolled out this technology, the Council races captured examples of it, they reverse engineered it to their purpose and Shepard became aware of it. That's a stretch.
I understand the difficulties of introducing a new game mechanic... a mechanic that probably improves the game... but once again, a few lines of dialogue inserted earlier basically clear it up (or spread the time line a little).
The reasons for this are many. It would, above all, hamper his ability to get the Reaper IFF. You suppose the Alliance would let him wander in and take it? That's assuming they weren't indoctrinated first. You may also recall that it was sucked into the nearby star right after. If you don't see how many problems this would've caused, how many delays and potential risks, then you don't want to.
It's only during the mission (when the Kinetic Barriers are brought up) that it becomes necessary to disable the Reaper Core and the Mass Effect drives. Prior to that it was just taking the IFF... of which the removal seems to have no consequences. There's no reason why before you arrive it wouldn't be prudent to message the Council or the Alliance and point out that while they don't seem to believe in the Reapers, reality itself does as there's one sitting right here... knowing that you would have escaped with what you wanted before anyone else came near.
There is nothing in the game to suggest the Collectors have more than one ship.
There's also nothing to suggest they don't... the ship is only identified as the same one 3 times out of 5 (I think) appearances. In addition EDi notes that she compared the ship to other "known Collector Vessel's" implying there are records of more than one.
In addition they seem to have a host of Oculus. Especially for the camping angle... why not have them sit exactly outside the Relay instead of mid debris field?
The Collectors have been busy with their experiments for some time. They probably didn't help out because their presence wouldn't have done anything to turn the tide of the battle. They were successful because their targets were weak and unprepared.
The addition of seeker swarms (at a time when there was no cure) wouldn't have helped Saren in the Citadel? A few more of them at Ilos wouldn't have meant that Shepard got nowhere near the Conduit?
As I recall, no one is "looking the other way". Craters are evidence that someone has been there, not of Collectors.
Which invalidates the "disappearing without a trace" aspect of the initial investigations...
Design oversight? Recovered from the first colony? Who knows? I never noticed this.
There were no seekers left on the first Colony and certainly no mention that you had captured one. It's a design oversight at best... and again, sloppy.
I have never noticed this, and can't seem to find it in any pictures.
The Cereberus logo is plastered all over it. A logo that Jack recognises on sight and is seemingly available on the extra net.
Also known as your personal opinion.
We're given a simple choice with no further options. Completely destroy the base or turn it over to Cerberus. No option to perhaps keep it for yourself as a forward operating base, no option to reveal it to the Alliance or Council etc etc. It's two choices that are massively limited... and conspicuously limited as well. Why wouldn't Shepard suggest leaving the base to the Council? Why wouldn't a Shepard who's been pretty independent in his play-through not want to keep the base himself? Why aren't we given an option?
As I say, it's no one massive glaring one... at least until Arrival... but there's enough little niggles that add up to frustrate me. I still enjoy the game, I enjoy the universe, I enjoy the setting... but I'd enjoy it more if my suspension of disbelief wasn't tested as often as it was.