The obvious It-Boy bone's-throw pandering of this notwithstanding, I can't see MBJ playing Clark Kent without some narrative tap-dancing (like, say, with that whole raised-by-Kansas-farmers thing, for one). As for Calvin Ellis, I'm willing to bet he doesn't have quite the purchase on the G.A.'s consciousness as Clark Kent (not to mention that whole President-of-the-United-States bit will probably just add fuel to the fire that would already be surrounding it at that point).
HOWEVER...since WB's apparently so willing to take another crack at a Supergirl movie after how big a dud the last one was, if they're so hot to slap that red cape and S-symbol on MBJ, why not give another Super-Family box-office flop from ye olden days another go and consider him for Steel? Granted, yeah, John in the comics is usually drawn taller than Clark is, but between MBJ's own physique and the armor I doubt it'd be all that much an issue with audiences; plus given his presence in animation I'd venture to guess he might have at least a little more exposure outside the comics than Calvin does. And hey, bonus point, it's another Superman-related character who isn't Superman, so I would think WB would just eat that up (don't worry, I'm sure they'd probably find some way to flout Superman's importance to Steel's origin and just reduce him to a name-drop or a backlit "faceless" cameo, and pat themselves on the back for their cleverness). Give him an actual villain from the comics to fight instead of another half-^$$ed screen-made villain (the White Rabbit would probably be a nice place to start), toss in some CGI'd polyalloy and throttle back on the fighting-to-destroy-the-weapons-he-created thread to shut up the "Iron Man Rip-Off!" screamers, and give him a nice long-handled plain ol' sledgehammer to shut up the "Thor Rip-Off!" screamers - actually, on that note, sticking to the whole John-Henry-The-Steel-Drivin'-Man motif wouldn't be a bad idea, either - and there you go.