Aqui ficam alguns sítios que explicam a diferença entre usar Factory ou Service no ionic e quando devemos usar um ou outro.
AngularJS : When to use service instead of factory:
Angular service or factory?
The old Factory vs Service question
https://forum.ionicframework.com/t/the-old-factory-vs-service-question/17678
https://forum.ionicframework.com/t/the-old-factory-vs-service-question/17678