Think of it this way. If there was " no destroy option, or anything in general, then it would alert Shepard, and the player that something is not right. There are to few war assets to help save Shepard if we take in the factor that depending on how many war assets you have, the more endings you unlock, and the final ending is the breath scene in Destroy. To my understand both assets and the number it projects is Shepard's willpower and war assets of course. The more assets, the more willpower Shepard and the player will have at the end. Shepard will not be so easily destroyed and converted into a Reaper agent, or a new Reaper if Shepard has large amounts of hope, and assets. I you have few assets, your Shepard is weak, and not " worth being used as a major figure for the Reapers plans. Your Shepard will just be another " pawn" like Saren and TIM, expandable if they choose to let your Shepard live.. In a way your Shepard thinks you have won, but in reality the Reapers destroyed Shepard if Shepard is not wiling to work with Synthesis or control, yet if only has the highest of high ems destroy, then the Reapers can't kill Shepard.
Not worth there time to use a weak Shepard, nor be bothered to let Shepard go, so with few assets to help save Shepard, then Shepard will die.
For control low EMS. You have taken note of controlling the Reapers " may be possible", yet if TIM was a pawn, the collectors, other Indoctrinated races, and Saren, and they thought they could work or rule the Reapers, they were wrong. Your Shepard is presented with the end that allows you to " take over" the Reapers, yet in the process it is you who is giving up control of Shepard, and the Reapers now have Shepard. Thought Shepard is a weak minded, and has very few assets for the Reapers to use or take out, Shepard is not " idolized, nor presented with a good outcome of him, or her being a "Reaper leader". In the every end you lose. Destroy low ems you lose, but your Shepard still held onto that belief that Destroying the Reapers is key to end the cycles, and the war with synthetics and organics for as long as it can last.
I don't understand what you mean about the third question, but if it is about why does the catalyst give you the option to choose depending on what you did with the crucible?
Well think of it this way. The catalyst wanted to allow Shepard to choose his, or her own path if they want the "perfect" Shepard the Reapers really want. However if Shepard needs to be taken out, then it may hurt the Reapers plans, but it's better to have the only being in the galaxy that could rally the galaxy and become the one thing to stop the Reapers, dead than alive. If you have low ems Control or Destroy, only one option is given, that your Shepard has thought about ever since you took out, or save the collector base. In this case, the Reapers do not even need to bother with using Shepard, but they can not allow Shepard to just get up and live to fight another day. It either ends in low EMS Destroy for Shepard, or in Control,have Shepard become a Reaper trooper, yet not that important to use. Much like a leader of Reaper ground troops instead.
For mid ems Control Destroy, and Destroy, Shepard is some what important, yet not that much of a thing to be afraid of. for Destroy the Reapers will still kill Shepard, yet it is harder to do so because Shepard's mind is still fighting, yet can still have hope. Yet it is not enough for Shepard to "live:" For control your Shepard has proven that maybe Shepard can be used as a figure ahead, but like TIM and Saren level. Not as a Reaper but a Spec ops agent/CIA agent in a way.
For high ems Control, Synthesis, and Destroy Shepard has reached the height for what the Reapers value, and fear. Shepard at this point can make it out alive, and recover from the indoctrination attempt yet the Reapers know this, and that is why a new ending appears. Synthesis. If Shepard chooses synthesis, Shepard becomes one with a Reaper capital ship, my guess would be Harbingers, if you look at it from an IT point of view. This way Shepard has let the Reapers take over "EVERYTHING" Shepard is and holds dear. Tis why it could very well be when you see the galaxy being synthesized, it is Shepard's body being converted and taken over, and viewing the Reapers ideas as "good, and awe like beings" For control, your Shepard can become a Destroyer Reaper for all his/her hard work in bringing the galaxy's only hope of a major retaliation, and a vast galactic leaders from every race, which can be used to Indoctrinate and be used as agents if they sub come to Reaper control. You surrender Shepard to the Reapers and that is all.
For destroy, Shepard has risen above any organic, and synthetic being in the galaxy in this cycle, or maybe from all or some past cycles ago. Shepard has been told many times not to trust the Reapers, and to destroy them. Yet with synthesis and control in his/her mind, the player/ Shepard's consensuses in a way, must help Shepard decide if this is the right path to save not just the galaxy, but Shepard to. By picking Destroy Shepard gives the Reapers hell, yet though the galaxy may live on without Shepard, Shepard didn't have enough assets to save him/her and died.
Now for the best ending to unlock if you want to rank them by unlocks by assets, it is the breath scene regardless if the EC lowered it. You had enough assets to save Shepard, and keep his/her mind intact.
Now what we can gather from this is the Reapers can not force Shepard to agree or see their way of thinking. They must persuade Shepard/the player to see how horrible destroy will be and how control and synthesis can save everyone, just they "ONLY" need Shepard to just do this one thing and all of this shall end. The player/Shepard has the choice to decide the galaxy,and Shepard's fate. For the crucible it is more like a test, rather than can it kill the Reapers, control them, or synthesis the galaxy. This is all about Shepard at this point. The sole reason why harbinger, and the Reapers were so hell bent on destroying Earth, hunting down the humans, and turning them into Reaper genetic material,and going after Shepard ever since the events after ME1. SO though upgrading it may help strength Shepard's will and war assets, if you think IT, then we have not seen the crucible really be used, and in this case, it could be a Reaper design to fool the organic races and synthetic races into believing the crucible would destroy or gain control of the Reapers. don't know, but it is just up for debate.