I agree with you Gav that the foot is not as protected. There is also a theory out there that it is to do with the layout of the studs i.e. they don't have the same number on each side therefore altering the biomechanics.
Problem being that most professional footballers are sponsored to wear particular boots, wether they are correct for them or not and its very hard top get them to change.
I remember when I was at a club, a boot company brought along their new design for the players to try out. The ones that opted to (and this was just for training) all ended up with soreness due to the boots. Players need to realise that they need to look after their feet and put them in the correct boot, not just a fashionable one or one with a huge chunk of money attached.