I think it has to do with the decline that started in 2000s when 3D graphics became the norm for most of the games, unfortunately for RPGs too. 3D graphics meant a lot of effort put into visual effects (and let's be honest, at the begining of 3D gfx cards the landscapes looked horrible compared to 2D pixel art) at the expense of game mechanics and complexity.
About the Fallouts, I'm not judging F:NV because I haven't played it, but FO it's a lot about atmosphere and tactical combat. With isometric map, you can plan an ambush at a door then count how many steps you need to take to cover around the corner of the house, before starting the fight. A FPS style engine is more superficial in terms of tactical combat since it's harder to predict in advance how long it would take to reach point X or if the enemies are going to come through point Y.
And let's not forget the style, since you mentioned it. To make a wild comparison, it's like a homage band to an old school heavy metal band, dressed in glam rock style.
From your mentioning that you weren't into isometric games until PoE I take it you are young, but the golden age of computer games was in the 90s, before today's AAA titles and big companies. Hell, by isometric I understand tile based maps, not hand drawn landscapes like in BG/PoE.