Consistency. Stop breaking your own rules, and stop breaking assumed rules. That is to say, if someone's going to write about aspects of the Alliance Military, make sure they have at least a passing understanding of military structure (or, if you're going to break from military structure, explain it). Don't say almost all space combat is done at thousands of kilometers and knife fights are rare, then show nothing but knife fights. Don't say guns devolved over the course of a year and suddenly we have to use ammo again, or an equivalent too it.
Don't put the cart before the horse in the creative department. You want to have epic close up space battles, make that your cannon. Say energy weapons have extremely short ranges and sensors aren't reliable at long ranges... you have a justification for nothing but knife fights and don't have to contradict yourself. But you went the other way. These things build up and by ME3, I frankly didn't believe you anymore.
Ashley Williams was a Gunnery Chief in ME1, a Lieutenant Commander in ME2. How? I don't remember her having 4 years of free time to get a degree, not to mention attend officer school and get through Ensign and Lieutenant first (also, Ensign wasn't a rank until ME3, where'd that come from?). Kaiden was a Staff Commander? We already know Commander is a field grade officer, so how is one a Staff Grade Field Grade officer? It makes no sense. Now, it's possible that Kaiden had the instance-use of Commander, meaning in-command-of-a-staff but that wouldn't make much sense to use when it's already a pay grade and we see no evidence that Kaiden is in charge of anything whatsoever.
On the other hand, if the Alliance Military structure is so vastly different from NATOs, there really should have been a codex or two about it. I can't help but chalk this up to lazy research.