Probably the best is indeed something like that. In a completely ideal world, a terminus for all Dublin would be under St Stephens Green, with underground connections to the DSER, MGWR, GNR and GSWR lines. Had the Luas Green / Harcourt St Line not have been (re)opened, they could even have used that very well to start going down underground while also providing a commuter service.
In such a scenario, with an underground "Dublin Central" (layout possibility?), the question would air as to whether the "Enterprise" and other main line trains would use Connolly / Howth Junction, or go under. Putting commuters unground would be an option just as much as the other way round.
To go to the thread title, Brexit will put any solution to the cross-border line back, in all likelihood.