If you start from scratch the easiest route is probably a default GraphQL setup. No real need for DDP or Meteor specific setup, unless you want to use the Meteor accounts system.
DDP-Apollo was created for Meteor users who already had an app and wanted to add GraphQL. It helps to get started quickly with support for Meteor specific APIs. For example, having a userId in your SimpleSchema or when you call a Meteor method within a resolver.
With a new app, you probably haven’t invested heavily in Meteor code yet and can go the default node/GraphQL route. A nice thing of DDP-Apollo is that subscriptions work out of the box, but you can set that up yourself as well.
So in short: use a default Apollo setup unless you already invested heavily in a Meteor specific app.