For me, the ending was just too nonsensical. Some of the very theories and ideas directly challenged the lore and some of it was just ridiculous. Here are my major gripes;
1) The reapers were created by the Leviathans to devise a solution to conflict. So despite the obvious illogic of creating death dealing robots powerful enough to destroy you to solve the problem of races being surpassed and killed by synthetics, the leviathans are shown as god like controllers of organics with the Leviathan of Dis in the DLC taking control of a Reaper and crashing it into the ocean. If they could do that, how did they lose? More importantly if they could indoctrinate any being provided it was in range of a space magic artifact (for all the sense that makes anyway) how did this problem arise. If you can control beings naturally it might be better to do that than build a super robot.
2) The Catalyst has no credence to its argument. It claims the reapers are there to restore order by exterminating organics which have the potential to build superior synthetics hence preventing chaos. It also claims to store the knowledge of the creatures inside the reapers. Firstly, assuming they made a reaper out of each race thats quarian, asari, volus, krogan, human, elcor, hanar, salarian, drell, turian, batarian and ive probably missed a couple but thats 11 races which equates to 11 reapers. Shepard killed three. Two are seen on screen dying in the space battle. There is no way the reapers can maintain that casualty to harvest ratio presuming shepard isnt the only one intelligent enough to say shoot the big glowy thing where it fires out of. They would be extinct within a few cycles. Secondly if they attack organics and leave synthetics alone then the synthetics will naturally develop to much higher levels than the organics instigating 'chaos' anyway. Thirdly why not target advanced synthetics, the whole universe probably wouldnt go to war with you if you blew up their mouthy toaster. Fourthly it says shepards presence changes the variables except for in terms of the catalysts logic shepard is junk data, an enemy with the capability to damage you only if you tell it what to do has no effect on the extermination of advanced organics to preserve order. The only way shepard could shift variables is if the reapers were programmed to allow an organic which reached their control core to take control, a line of code which any logical AI would remove or alter as soon as it concluded organics were the problem, or if their logic of synthetics surpassing organics had been disproved by Shepards presence which would either lead to a hardware and software upgrade (retreat and rearm in military terms) or them telling shepard to prove he had surpassed them by actually operating the damn thing. This wouldnt be logical anyway as they moved the citadel to earth so they could defend it. Furthermore the catalyst stipulates that the universe will be better for its actions except the majority of wars were organic fighting organic and the very fact it leads a synthetic army to kill organics to stop synthetics killing organics is nonsense.
3) The illusive man. The catalyst states he wasnt expecting shepard so WTF is the illusive man doing standing on the citadel at random semi-converted and spouting nonsense. If he was positioned there to stop people breaching the control centre then why was he by himself and who were they expecting? If he wasnt what was the purpose of having an indoctrinated half-husk wandering around like an idiot in the bowels of your control centre? If he can control people then why didnt he control shepard before and stop him destroying cerberus along with Kai Leng, and if he just acquired the power why was he gifted with it when the collectors who had been indoctrinated since the last cycle had no such ability?
4) The collectors [mass effect 2 ending]. The number of collectors you fight on the ship is about equal to the collectors encountered elsewhere so either the collectors had an incredibly small army, were incapable of defending the reaper they had been indoctrinated to build in the first place or were all elsewhere for no reason. Also why did they conduct research on current organics, what was the purpose? What did the reapers do with them all? Surely they were a useful asset to defend the reapers particularly considering the protheans sent 900,000 of their own into stasis (Javik confirms this) and the collectors were prothean at one point as well as their being prothean seperatists. This means the protheans who were far more advanced than any current cycle races were incapable of defeating the collectors who are clearly shown to have enormous numbers. They probably thought of nuking the ship as well. Furthermore the collector numbers couldnt have decreased much as they are so rare in the current cycle in ME2 most species consider them a myth.
5) The beam. just why? Even a child could tell you beaming people into the only thing capable of defeating you is a terrible idea. Also, if soldiers start actively targeting the beam presuming you are stupid enough to not beam them onto an irrelevant nearby ship or so forth, why not shut it off. Its clearly possible because you turned the thing on.
6) The choices. Synthesis being the stupidest. How is that possible? HYBRID DNA????? AI has no DNA, its codes and protocols. By definition hybridisation is cybernetic alterations which is simply putting machinery into people. Machines cannot be given DNA or a body or flesh or blood, putting DNA into a machine is like putting a cat into cement. Yeah its in there but serves no purpose. Machines cannot do anything with genetic code, and people with machinery inside them do not have different DNA because of it. Therefore the solution is circular because synthetics still exist and organics still exist so conflict will according to the catalyst eventually arise. Even presuming the symbiosis is possible then what is to stop the synthorganics from creating pure AI? Control, how would it work exactly and why would it kill shepard? when inside the geth platfom to delete the reaper code his body was in stasis hence he could run the reapers from stasis using the platform conversion stored inside every one of the thousands of geth currently attacking or could have the catalyst realign the parameters as the platform used by the geth was created with reaper code anyway. Also he was standing by a control panel. And there was a control panel below him. Not that hard to link the software to either giving him control and his body. Destruction, he randomly ends up on earth. The reapers die. The reapers told him how to kill them. Is it technically suicide?
7) Shepards armour. A reaper beam hits him, he loses his helmet as well as most of his armour but has no physical damage except a headache? Since when was his armour held together by velcro? Oh and despite being knocked back by the reaper he ends up closer to the beam.
There are more but these are the main ones. I loved the game and appreciated the ending at face value. It was just the fact the choices were all stupid, the way he was given them was illogical and the decisions you had made up to that point were irrelevant. having said that it hasnt turned me off getting another mass effect game, unlike the horrible lag of fallout which has turned me away from future titles.