To answer you closing statement:
1. Seeing war assets in action is a perfectly normal expectation.
2. Story problems do exist. Harbinger flying away without firing at the Normandy? Why did Mr. Catalyst need Sovereign to activate the Citadel Relay if he "is" the Citadel?
3. Details are always relevant in storytelling; thus, inconsistencies are relevant.
4. It is a game that is not Xenosaga and was not made by Hideo Kojima; there is a natural expectation of gameplay.
Furthermore, your understanding of Hegel's dialectic is pedestrian. Hegel only used thesis, antithesis, synthesis when describing a dialectic he attributed to Kant. Hegel's dialectic was abstract, negative, concrete. The actual German word he uses for the third step--what you call synthesis--is "Aufhebung." Sublimation probably captures his intended meaning the best. You seem to have based your analysis entirely on the use of the word "synthesis" and the fact that there are three options presented. Synthesis is a perfectly normal word for describing the combination of two things, and a set of three is hardly a rare occurrence in well, anything. Your analysis is also rather shallow in that his dialectic was meant to be general enough to apply to everything, so it should be widely applicable, even to things not intended to be.
In fact, let me have a go with another blue, green, and red trio:
Bubbles (abstract): You should be nice to everyone.
Buttercup (negative): You gotta be tough and mean to survive.
Blossom (concrete): You should be nice normally, but tough when you need to kick butt and save Townsville.
I have now proven that Craig McCracken based his design of the Powerpuff Girls off of Hegel's dialectic.