They were gone for roughly 17 years. Their final appearance in the 1990s was in Hotel Mario which released in 1994 (if you even want to count that as a real game), they were gone until Superstar Saga in 2003 (showing up as just filler bosses at the very end), and then reappeared in 2012 and have stayed around regularly since. That's an 18 year gap between 1994 and 2012 where they only showed up once, so 17 years total where they didn't show up at all. They've been in around 16 games (two of which were just... well they're Hotel Mario and Mario is Missing lol, one is a NSMBU rehash, the Luigi version). If you look at the bigger picture of how many Mario games there are and then look at how many the Koopalings have appeared in, they really haven't shown up much at all.
I'm not trying to sound like an *** but the Koopalings actually had effort put into them this time around. Their boss fights are all unique and their dialogue, while limited, is enough to tell you that each one is different. At this point, anyone saying they're all the same because they're all the same species might as well say that Mario, Luigi, Wario, Waluigi, Peach, Daisy and Rosalina are all the same because they're human.
I'm totally fine with older, established characters showing up for the first time ever in an AU and getting much needed development. I'd agree with the "they're getting old" accusation if their battles were all the same and they had 0 effort put into them.
I guess tl;dr, what I'm trying to say is that this game has plenty of faults and lots of room for improvement but the Koopalings are not the issue here. I personally would love to see Paper Mario go back to its roots by bringing back battles that are more TTYD style, along with new partner characters and unique bosses and whatnot. But Nintendo seems to have made it clear that as of now, that's not happening.