A weapons platform (like a ship or tank) needs a combination of 3 factors. Speed of maneuver, strength of Armour and power of weapons with the specialized targeting systems required to utilize them more effectively than the opposing force. Any deficiency in any of these areas is not compensated by strength in one area.
That's kinda interesting, because the usual consensus on this sort of thing is that you have to 'pick two'; you
can't have superlative speed/maneuverability, armor,
and firepower/accuracy in a single platform.
In a subsequent post, the battlecruiser came up, which is also interesting, because I think it's one of the perfect examples of how this sort of thing can actually make a great deal of sense.
In the Great War, British naval doctrine of the Fisherite paradigm was oriented toward the employment of a fast fleet that could hit hard. It was designed for a global mission: the Royal Navy could be anywhere in the world faster than anybody else and kill whatever it needed to kill when it got there. Whereas German construction tended toward vessels that sacrificed some speed and weight of broadside in favor of superior armor (while also making up other deficits with superior organization, training, and fire control); it was designed for a more circumscribed mission, defensive operations in the North Sea.
The nature of North Sea fighting meant that German vessels tended to have technical advantages over their British adversaries, but those technical advantages were rarely leveraged well due to a combination of deficient strategy and bad luck. By comparison, the Royal Navy's technical problems in the North Sea ended up being irrelevant because of its technical superiority in other areas; the battle fleet's speed meant that it was possible to concentrate more rapidly in time and space than the Germans could. When the Grand Fleet dispatched its battle cruisers to destroy Spee's Asiatic Squadron in the aftermath of Coronel, that theoretically created an opening that the High Seas Fleet could have exploited - but the British had a relative mobility advantage over the Germans, and utilized it to concentrate against Spee before anything went pear-shaped in the North Sea.
So while Britain's battlecruisers were often death-traps in the North Sea battles, that misses the point. They weren't really designed for the North Sea battles, which the Royal Navy probably shouldn't have fought anyway. And the operation for which they really
were designed, the Falkland Islands battle, was executed perfectly: no ships lost, with only 30 British sailors killed and wounded, in exchange for the total annihilation of Spee's Asiatic Squadron. Had the High Seas Fleet been able to concentrate against the Grand Fleet by using the Asiatic Squadron as bait to convince the British to divide their forces, things might have gotten very bad for the British in a hurry - especially considering the attrition that the Grand Fleet's battle line had already suffered due to the U-boat terror of fall/winter 1914. But the Germans were unable to capitalize on the short window that they had, and the British escaped quite handily.
I don't know that this has much bearing on the Reaper War. Battlecruisers were purpose-designed warships. Arming the liveships with big guns wouldn't make them into battlecruisers; they might have had big guns, but they would still presumably be much less well-protected and much slower, and they would still be crewed by non-military personnel. The only thing that connects the two ideas is the umbrella "glass cannon", and these are as different a pair of glass cannons as it's possible to get.
No one will convince me that it is stupid or silly to expect that experienced, professional writers follow through and pay close attention to detail with the elements that they created. That is the sort of thing that you see in the worst types of fan fiction; not in an award winning work of art created over a period of years by highly qualified creative minds. In the end, these liberties that the creative minds in Bioware took, with the rules they themselves set-up, tends to make their attempts at installing dramatic tension fall apart for me, cause me to recoil out of the story and shatter my suspension of disbelief more than engage me in the story.
That's fair for you.
My perspective on the matter is this: virtually no fictional setting has fully worked-in elements that make sense anyway. BioWare's hardly alone here. Academic history, anthropology, physics, all those things - they're kind of, y'know, hard subjects, otherwise you wouldn't need to undergo academic training to 'get' them.
And continuity isn't much different. Fundamentally, the setting is a vehicle for the story; it contextualizes it, complements it, and so on, but 'lore' is ultimately a secondary consideration. Continuity is clay for the writers to tell the story that they want to tell; if they want to tell different stories in subsequent books or games or movies or whatever, they can and will change continuity as they like. If they maintain continuity throughout, well, cool, but if they don't, that's...well, it's not exactly like nobody else does it. Besides, if we saw space battles that looked like the ME Codex's battles, or if biotics were used the way the Codex says they have to be, then the game would be much more boring. It wouldn't look as cool or play as cool.
Since virtually all fictional settings are going to violate continuity or plausibility at some point or other, the question mostly becomes 'what can you personally deal with before your suspension of disbelief is broken?' As you say, the geth-quarian conflict breaks your suspension of disbelief and prevents you from enjoying the setting, and I'm sorry to hear that. But it doesn't work that way for other fans, and it's not because we think that it's totally believable - we just don't really care.