I don't think I've seen a single of the "dozens of plot holes" that keep getting brought up that I couldn't easily refute. Of course, I haven't bothered to learn the codex by heart, so I can't comment on the internal consistency, and trying to argue with you guys would be about as fruitful as pissing into the wind, but I'll address the point of "boohoo, the space battles aren't as they should be according to the codex!!11"
1) Codex explanation is for how dreadnoughts, the biggest ships do battle. We've only seen two, destiny ascension and Sovereign.
2) The "battle" for citadel is, of course, different from the norm since it has Sovereign not even attempting to take out Destiny Ascension, but instead making a straight beeline for the Presidium tower (and ASSUMING DIRECT CONTROL of its systems).
3) Normandy vs. Collector cruiser has no dreadnoughts and has a recon ship fight a medium sized cruiser on both occasions. First time by getting ambushed, the second time by ambushing it.
Problem deconstructed and dismissed (like the Reapers). Which one should I do next?