I think Nemesis is still very well-liked, on the whole, even though it doesn’t quite stack up to Smiler and Wicker Man in popularity terms; I can imagine that the ride’s high throughput is at least part of the cause of its lower queues. Although I will digress that it is not the most popular among the average visitor these days, it does still have considerable appeal, and it doesn’t stand out to me as “the least popular attraction by some margin” by any means.
Also, Nemesis’ removal would almost definitely cause mass uproar among enthusiasts, greater than even that of some other recent ride removals; you might have thought that the reaction to Blackpool’s Wild Mouse removal was bad, but the reaction to Nemesis’ removal would likely be 10 times worse!
I think the reason a Nemesis retrack is being suggested is because rumours have been spreading that it’s in a somewhat ropy state, and rightly or wrongly, many consider the ride somewhat irreplaceable. There is a precedent for Merlin doing this, with both Gardaland (Shaman) and Heide Park (Colossos) having had coasters retracked in a similar fashion recently. My logic is; if they did it for Gardaland’s stock model Vekoma Corkscrew, which wasn’t exactly a revered ride prior to the retrack, I definitely think they’d do it for Nemesis!