Very low cost automatic transmissions are terrible - the gap between gear shifts goes on for ages. The Vauxhall Corsa is an example of this; for the American market check out a Smart Car.
Is this really a good argument against automatics though? The worst example of anything is usually going to be pretty bad.
As a matter of current economics, yes, if you have a very tight budget and want a good driving experience, manual is going to be better. But automatics are as fast and as efficient as manuals a little higher up the market. And it will trickle down soon enough.