Once Amuro Ray picks up the Nu Gundam, he'll be able to dodge anything, plus take out any enemy 9 squares away with a 1200 power Fin Funnel, up to twice per turn once his character level gets into the mid- or upper-30's.
Daitarn 3 has a high HP pool and armor, with its Sun Attack being the strongest technique in your arsenal for quite some time, if not period. Its only weakness is that Banjou Haran does not have the "Accelerate" Spirit Command.
Scrappy Level: Any scenario where a battleship requires protection. These usually suck because the ship cannot move, has poor armor and barely any chance of evading attacks.
That One Level: The final scenario "Ragnarok". You're on a map with a total of only three enemy units, two of which are the infamous Valsion (the Final Boss mecha of Super Robot Wars 2), and the other being the True Final Boss, Shu Shirakawa and his Neo Granzon. Now count the facts that in this game, "Focus" and "Valor" are RARE Spirit Commands, unit upgrades don't account for mobility or weapons, Will-raising Spirit Commands had a prohibitively large cost and the two Valsions were weak enough to die in a few hits without effectively raising your pilots' Will. Add the fact that Shu can raise his Will by at least 15 each turn due to your characters attacking him (not counting any allied units shot down), can attack TWICE each turn (as does your units, but it's more like "get twice the chances of getting shot down"), had insanely high HP and armor, with a Will cap at 200, whereas your units hardly exceed 150. In other words, EVERY SINGLE ATTACK WOULD KILL ANY ALLIED UNIT RIGHT AWAY...
Part of the difficulty comes from not paying enough attention to how Will in 3 works. In short, a bunch of weaklings ganging up on an uber robot equates to scrap metal. It's true during the whole game, but it's the most apparent in this scenario.