Well, the problem with using auto-neg for 10/100 links is that there is no real standard and they frequently do not correctly
negotiate a good link in a cross vendor application.
I've never had a successful auto-neg 10/100 link come up full speed and duplex between Cisco and Juniper. Hence the need for turning auto-neg off and setting the speed and duplex explicitly which does work.
I'm really surprised that someone thought this was a good idea to remove.