Holy Crap. I had forgotten, wasn't their an Ammo mod that ignored shields in ME1? Or am I mistaken?
Wait, yep they had those, they should have used them.
I think I know what you're talking about, and that mod didn't ignore shields, it just made it easier to punch through them. Besides, those were for small arms, and its more complicated than you think to adapt them for big guns. Also remember that until the invasion itself happened, not a lot of people took Shepard seriously, and by then it was too late to modify the big guns or prepare in any other way.
Also know that they wouldn't have had a large stockpile of "outlawed" WMD's, as that would've defeated the purpose of having them outlawed. There were mentions of nuclear weapons used, but that was mainly by Cerberus though. Aria mentioned that the mercs would've used outlawed weapons, so its possible there were battles we didn't see that involved said outlawed weapons.
Either way, the issue wasn't weaponry, it was lack of preparation. The various races did so bad because the Reapers took them by complete surprise, and overran them before they could organize and regroup. You could have the most badass firepower out there, but if you're not even prepared and completely ignorant of the threat, it won't do you any good.