I'm not concerned about this. Mechanics-wise, it's not that there was no precedence - J and W had Nadesico and FMP, which have pretty low-powered and realistic reals (well, except for Lambda Driver) fighting alongside Mazinkaiser. And the Alpha series had both tiny Valkyrie Fighters and the taking-on-millions-and-winning Gunbuster. Sometimes this even happens within boundaries of one series, like in Overman King Gainer.
As for the series feel, the cynical and idealistic series clashing with each other is a lot of fun in SRW! Well, when you can understand what is going on.
And yeah, Armageddon is pretty grimdark itself. Shouldn't they go with the Shin vs Neo version? Not that I mind but it should be easier to incorporate.