I'm in favour of Metrolink conversion for Atherton, but it would need a new entry into Wigan, perhaps using part of the former line that bypassed Wallgate, then running on street to enter the town from the south, if that's possible. Hindley has room for 2 heavy rail and 2 Metrolink tracks but is not well laid out for interchange between them, which would involve climbing stairs. From the former junction for the Pemberton loop, there are only 2 tracks into Wigan.
At the other end, it's hard to see how you could provide a decent interchange in the Salford Crescent area. I've often wished that Pendleton Broad Street had been chosen as the site for an interchange, as it has two long island platforms, each wider than Salford Crescent. If the Agecroft Connecting Line (38 chains long) had been retained and upgraded , trains to/from the Bolton line could have used this route and the two centre roads at Pendleton BS, while the up Atherton line could have been raised on to a flyover from Irlams o'the Height to Brindle Heath Jn, the up and down Atherton lines serving the outer faces of the island platforms. How you would disentangle them at the other end I can't say. But the platforms at PBS look longer than the island at Salford Crescent, which is both a miserable place in itself and a constraint on potential train lengths all over the northwest. On the other hand, Salford Crescent is more convenient for the University and it has a useful if slow bus connection to the Lowry (at least for matinees, I've never risked it at night). Anyway, it's too late now as the Agecroft route has long gone.