If you were to use only the new skill, you would lose some of the more detailed functionality from the old skill. Examples that aren't replicable in the Smart Home skill:
tune ABC in the Office
set the volume to -45.5 db
skip 6 times
mute the Guest Room
go to the next chapter
These are just examples. Smart Home Skills do not really have a syntax. They just have "turn on", "turn off", "set XX to Y%". They're not capable of the intricate control of custom skills. We have made volume work with all devices on a percentage basis with the Smart Home Skill, so you can say things like "set the Denon Receiver to 50%" and that will be converted to the appropriate decimal volume that is 50% between -80.0db and +18.0db, but you can't use the direct volumes like in the custom skill. Also, the many different play/pause/next/previous and chapter control from the custom skill can't be replicated. Finally, all of the custom channel commands for ABC, channel number 456, Food TV, and many others require the custom skill.
So I think the best of both worlds at this point is just link both skills. For all the basics, use the Smart Home Skill because it presents Activity Names in a more straightforward way. Anything on/off is much better. Then for channels, volumes, and specific commands like pause, use the custom skill syntax.