I tend to make pregens when we play new games. I usually get an idea of what the players want to do, but make up the PCs so that they "fit".
the biggest advantage of pregens is that it aves time at the table. I run games that meet, if we are lucky, every three weeks or so. I don't want to lose a whole first session creating characters. It is not so bad when we play D&D, since pretty much everyone has the books and can create their character before the first session -- so long as they let me know what they are playing. But when we played Exalted, we lost half the first session just explaining characters and having them spend their bonus points. I can't imagine trying to guide five players in full character gen in a game like that.
As far as only taking pregens through a one shot or a mini-campaign, or that pregens are somehow not as close to a player's heart as a character he designed himself: do not concur. A player will make a character his own without any trouble, regardless of what is on the sheet. Hopefully, he does so by using what is one the sheet, but we all know players whose characters -- all of them -- hyave the same personalities, regardless of race or class or level of experience.