My suggestion is to first see which holds your interest. Second thing to do is to check the job profiles that you are interested in and then decide which you would like to go for. Embedded systems has wider opportunities while automotice may have slightly lesser options. But again I would suggest that you should do some research while deciding like checking job profiles, syllabus covered in MS and your interests rather than someone telling you what their opinion is. 

Hey,

After doing B.Tech in Electronics and communication, you can choose any of the courses you mentioned for MS degree. 
Both the courses "embedded system" and "automotive electronics" are the subfields of electronics and communication engineering and both are good.
• So go with your interest. Where your interest lies, that will be the best course for you.

• MS in Embedded system focuses on the designing of hardware and software that control a device, process or system.
• MS in automotive electronics deals with the study of electronic systems used in road vehicles.

Here you'll find more about electronics and communication engineering -: 
https://engineering.careers360.com/electronics-and-communication-engineering-0?amp

Hope it helps!