They haven't, not in the same way. But it's not like Xenogears couldn't be surpassed in certain elements, it's just that the entire mix of it all hasn't been topped by any of the later games.
Xenosaga Episode 1 vastly improved the cinematics of the game, and the dialogue quality was improved. I also really liked the encyclopedia they added for that game. But, the gameplay was worse than Xenogears, there were long treks with little chance to replenish items - the Encephalon was nightmare. Another gripe I had with this one was how big and empty a lot of the civilian areas were, particularly like the space ships.
Xenosaga Episode 2 improved the pacing of gameplay. There was nothing crazy like the Encephalon, but virtually every other element fell short of the first Xenoblade. The biggest thing for me was that the cinematics were no longer as entertaining. Also, the art style was weird, Xenosaga 1 seemed the logical progression from Xenogears in terms of art, but Xenosaga 2 seemed like some kind of soulless Tales of spinoff. Many people didn't like the tougher enemy battles, I wasn't bothered by it, because the game itself had like 125-150 battles in it total as opposed to the 300-500 in the first game. Also, it wasn't some convoluted battle system like Xenoblade Chronicles 2 (but we'll get to that later). Episode 2 and 3 lacked Mitsuda, which hurt.
Xenosaga Episode 3 - it wraps up the story really fast. I did like the locations, I didn't like the production value which felt amateurish compared to either Episode 1 or 2. The emotional impact of the ending was excellent, but the journey there could have been much more satisfying. The game had the advantage of wrapping up the story, but I preferred disk 2 of Xenogears to Xenosaga Episode 3... which is really what the game was.
Xenoblade Chronicles dramnatically improved the gameplay, the dialogue, the voice acting and production was much better than Xenosaga, but I felt the story declined. Basically, the story just took the plot of Fei, and re-wrote it for the new setting and elements, swapping out stuff like Weltall for the Monado, Combining Alice and Elly and then swapping them out for Fiora, etc.. The story felt more slender and bare bones. I think because I was already familiar with Xenogears that I wanted more. Xenoblade Chronicles felt like diet Xenogears in that regard. Still, many elements in this game were fantastic. The gameplay had never been better, it carried the game to a comfortable 90-120 hours worth of play time, that's rare in an RPG. Some of the locations were fantastic, like Fallen Arm and Frontier Village... but the cities weren't as magical as Solaris, Zeboim civilization, or Bledavik. Still, some parts of the story were magical in ways Xenogears was. Also, Mitsuda was back on this one. One big problem I had with towns in this game aside from the aforementioned, were that they were too large and spread out - it was a similar problem to a lot of the Xenosaga Episode 1 locations, particularly the spaceships.
Xenoblade Chronicles X, I loved this game, it was the first "Open world game where you can go everywhere you can see" game from Nintendo, the prototype for Breath of the Wild. It was a little rough, especially in the audio department, but back were the Xenogears/Xenosaga Episode 1 style visuals, which I really appreciated... Gone was the Mitsuda soundtrack, and it was instead replaced by the guy who did Assault on Titan, and while I liked some of the songs, this guy is not a video game composer, and fell quite a bit short of Mitsuda. I liked the story better in this game than Chronicles 1 - human city transported to an alien planet, help the new civilization thrive. I also really liked the more open gameplay. Battles were more straight forward than the first game, and also a little more advanced. It featured a more open quest system, and the ability to kind of shape your own story while the grand narrative fell more to the background. It was a unique experience that I'd never come across before in a game. This one wasn't as popular as the other two Xenoblade games, but it's my favourite of the three, and my second favourite Xeno game. Also, New LA is one of the greatest cities in video game history - but I've only come across a couple of others on a similar scale, both are in Witcher 3.
Xenoblade Chronicles 2, I got sick of the gameplay. It felt a little bloated, repetitive. I just wanted something much more straight forward and strategic like the previous games. This one felt like completing a puzzle and damage would pop out, and the strategy was based around which elements in the puzzle you'd focus on. It's much more satisfying to just select a fire spell to burn paper then do some kind of 4-6 command chain to achieve the same thing. I also didn't like all the locks, because I was never sure if I could find what I needed for the keys, or if this was New Game + stuff, so I ended up just avoiding all of that content, and never seeing it. The towns in Xenoblade Chronicles 2 were a lot better, the art didn't remind me of a "Xeno" game at all. It looks a lot like that Netflix anime "Expelled from Paradise." It's just a bit too cartoony for me, and Rex looks like a kid. But pluses for me from this game include: my favourite towns (aside from New LA and Frontier Village) since Xenogears, and I like how there are a lot of towns rather than just 1 or 2 good ones, with the others being mediocre - which has been the case from Xenosaga Episode 1 onward (which had the Kukai Foundation, and then a lot of ho-hum towns).
Anyway, as a whole package, yes, Xenogears is my favourite. (apologies for mistakes/stupid grammar, wrote it fast, no time to proofread)
Also, I'll also note that Resonant Arc did a very good job in their research, but they do blame some of the sloppy stuff on Tetsuya Takahashi when it was Masato Kato who was responsible for all of the bad comedy in Xenogears, and also a lot of the bad event design choices. And it's almost certainly it wasn't edited by Takahashi or Saga because the timelines didn't allow for a proper dev cycle. The game is gigantic.
