So, there are megadei, and then there are megadei.
Been trying to figure out what makes the difference between "bigs" and their lesser megadei cousins. FWIW, got a chuckle out of Wikipedia's megadeus listing, pretty sure Osrail got toasted by eye lasers and not chromebuster, but it's been a while.
From Ep. 2 we know that "megadei" is a generic name for armoured attack "robots." Not sure if "robot" would really be the correct term, or if they'd be better off characterised as an armoured exoskeleton with a semi-sentient AI. They appear able to function without a pilot, but seem very limited in capabilities without the pilot. Having watched all 26 episodes, I can't remember seeing an unpiloted megadei ever really take evasive action or take any autonomous self-preservation action. One possible exception could be Big O's turtling during the fight with Bonaparte while Roger goes off the Grand Central Station.
A curious scene is when Bonaparte first encounters Big Fau... I swear, for a second it seems like the writers/animators gave Bonaparte an "Oh Sh*t" reaction to Big Fau's apperance even before it breaks the surface. Combination of sounds and what seem like facial expressions seem, at least to me, to say "I'm screwed, I'm so screwed." As similar scene occurs shortly before Big Fau engages.
Anyhow, it seems that one major difference is in the level of weaponry displayed and used. Of course, this could merely be a product of unpiloted units versus somebody in the cockpit who knows what he/she is doing.
While there seems to be a massive difference in armoured plating between the units, that doesn't seem to be the issue either. Some of those other megadei have pretty tough skins.
Perhaps the ultimate difference between the Bigs and the rest is plotline "god mode." 
Will type more later.
Well, there is the archetype in Ep. 4, which looks to be pretty much a a primitive model. Always been curious about the Archetype's lack of armour coverage. Was it never installed? Did it get stripped for spare parts? Was it ineffective and get made into Paradigm Wheeled Fighting Vehicles? 
Leviathan also appears to be somewhat incomplete. IIRC it too had no real plating.
Behemoth of course had big gaping holes in the sides.
FWIW, Glenda has a pretty humanoid form.
Not sure if Eumenides really would qualify as a megadeus.
The memories thing is interesting, but note that the megadeus from the "Sea Titan" episode supposedly had memories... remember Angel yelling to not take its head out, to not take out its memories. Also, the unit seemed to be hunting for its long-gone pilot.
Do note that the weapon spread on the "bigs" seems to be greater than any of the others. A long-range heavy energy component with energy shield type device on Big Fau. A selection of short-medium range weapons on Big O. Long range missle ordnance on Big Duo (though the leg missles seem a bit... weak). All bigs seem to feature the eye lasers, with Big Venus apparently having what seem to be laser emitters in the "mouth" area.
Of course, there could be other weapon systems on the non-"bigs," but without a pilot, they may go unused.
. The megadeus does not show any capability of using those on its own.
Also, those flash backs show that the "Bigs" weren't necessarily invulnerable.
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