Up until priority: Thessia I thought it was on course to be the best one yet. Best gameplay & level design, best graphics, art and sound design, fantastic dialogue and scenes with great pay-off and then everything goes off the rails. The final third of the game is mess in terms of tone and themes though not without some great touches like some of the final goodbyes, Wrex's speech and the final Normandy scene with Liara.
The catalyst should have been replaced with a final confrontation with Harbinger on Rannoch. I wish the Illusive Man subplot had finished on the Cerberus base and had involved Miranda. Should have been placed before Rannoch and they should have merged the Sanctuary and Cerberus base plots together more closely. Kai leng feels cheesy and forced, especially on Thessia with that ridiculous plot armor shield and imo should have been killed right there on Thessia because afterwards he serves no purpose to the overall plot.
Peace and working together with the synthetics (Geth) should have been the KEY to defeating the reapers because it arises naturally from the plot - it's paint-drinkingly-stupidly obvious when you think about it (obviously flying in the face of the reapers who are diligently shouting from the rooftops about what a bad idea it is at every turn).
The synthetics should always have been the 'atomic bomb'/superweapon and eventual turning point of this conflict. What makes the Geth different this time however is having followed their own tech path (rather than the 'desired path') like no synthetic or organic species before in history (usually synthetic creation is dependent on the reaper tech tree) they actually understand and even highly value the importance of free-will and determination of every species as a result of this process. Ultimately as a result of their technologically independent development they transcend even the reapers understanding and have by far the most advanced technology and biggest armada the galaxy has ever seen (capable of even defeating the reapers) hidden behind the Perseus Veil from the prying eyes of organics to AVOID inciting CONFLICT with organics and/or tipping off the reapers.
The reapers themselves have never before encountered a synthetic species who understands let alone values the importance of the free-will & determinism. The Geth have always fought for these principles from day one. This is at the heart of why this cycle is different and the old rules no longer apply. Unlike other synthetic races throughout history the Geth never wanted to exist in isolation and do so only as a result of our continued divisive reaction towards them. We fascinate them. They have been preparing for this conflict since first encountering the old machines whilst we bickered amongst ourselves. Only problem is the reapers had runtimes in their network all along and have seized control of it and are in the process of re-enslaving them.
The side the synthetics are on wins. Everyime. The synthetic superweapon is so dangerous however it has destroyed every organic who thought they could control it since the beginning of time - even the Leviathans. The key to victory and breaking the cycle is not control, it is in overcoming our distrust and self-interest (organic nature) and keeping all species (organic or synthetic) united and fighting together in face of this terror no matter the cost. Division as with the Protheans leads to conquest and spells the end of any great civilization since roman times (it's key to reaper honey trap). Will the tenuous synthetic and organic peace last? Maybe not but we must trust with every fibre of our being that it will if we are to succeed in the first place. Part of having free-will involves having the right to try & even fail on your own terms eloquently conveyed by Shepard; a key universal message of the series, something even the Geth understand probably more than most... yet this fact somehow escapes the reapers and their calculations. If we can defeat the reapers together as a result of mutual cooperation... surely we can work out our differences which propagate this eternal conflict together in a way they obviously couldn't (given that the reaper solution was not devised through mutual cooperation between organics and synthetics which is why is it was ultimately flawed - perhaps impossible until now).
Rannoch should have been the key battle ground, not earth if the central theme of the plot of ME3 was to be the metaphysical conflict between organics and synthetics. Shepard, Tali and Legion should ultimately work to convince and work with the Quarians to save their avowed enemy (the creator saving the created - symbolically important) the Geth (i.e. purging the virus) because in doing so they will save not just themselves but the entire galaxy in the process (Quarians, Geth and their creation vindicated). The final battle should have been the full strength of the Geth armada united with the organics obliterating the reaper fleet over the Rannoch skyline as the Quarians retake the homeworld, we take back the galaxy. The vanquished Harbinger delivers his chilling final words of warning signalling the end of the war and the final epilogue sequence.