Not at all.
They're smaller because someone at Metrolinx bought into the marketing wank about "light metro" systems, and was able to convince their higher ups that it's somehow better to build an entirely new system from scratch rather than use existing standards with tie-ins to existing infrastructure to save on costs where applicable.
Should the track layout be designed correctly (and the signal system is upgraded to suit), there's no reason why Toronto's existing subways couldn't operate at the same headways as the Ontario Line. As with the existing trains enclosing a considerably bigger internal volume, there would therefore be a correspondingly bigger capacity for the full system as well.
Will the Ontario Line equal the capacity of the Yonge Line? Potentially. But it's going to cost all of us a hell of a lot of money to do it, arguably more than it would have been otherwise.
Dan