So I understand this sounds a little one sided but I think Terry stands a chance! What do you guys think?
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I side with Batman Beyond.
Young Justice as a whole is great, given what a broad representation of the DCU it is in animated form and for other reasons.
But, Batman Beyond is part of the DCAU (my favorite iteration of the DCU next to the comics), features absolutely fantastic music (Bruce Timm advised us to "Play it LOUD!"in the notes of the soundtrack), it advances the narrative of the DCAU and its been highly influential on the comic based DCU as well.
Not too shabby, Batman Beyond. Not too shabby at all.
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Are we comparing the shows or contemplating another Meta Madness Matchup? 
If the former, for me, Young Justice handily beats Batman Beyond.
I mean, I adore Terry, Old Bruce and Ace, but not in the same way I love Dick, Wally, Connor, Kaldur, Megan and Artemis. There were some truly spectacular BB episodes - but there were also a lot of clunkers along the way. Young Justice, on the other hand, is consistently awesome (again, in my book). Nothing from BB reaches the Zenith of YJ’s Misplaced, Bloodlines, or Auld Acquaintance. And while Terry certainly matured through his three seasons, I think we’ve seen far more growth from the YJ crew thanks to the time-skips. We’ve certainly seen a deeper, farther, wider DC universe than we got in Batman Beyond (though Neo Gotham was pretty schway). And - while I know this is sacrilege to some, I prefer Phil Bourassa’s design aesthetic to that of Bruce Timm.
However, I’m open to alternative views. Perhaps I’ll change my mind as I rewatch all three seasons of BB on DCU in HD starting TODAY! 
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big long connected stories like we see in Young Justice just wasn’t as popular when Batman Beyond was around. Young Justice is amazing and certainly is a improvement compared to some of the other new crappy cartoons we see these days. however back when Batman Beyond was new it was the Young Justice of it’s time, I grew up with that show and it was a very dark Batman series with quite a few twisted surprises for a cartoon back then. so I say they are kind of tied at this point, both shows have amazing qualities but they are from two complete different times. Batman Beyond went from 1999 through 2001 kind of holding on to the way a lot of 90’s super hero shows were but it certainly pushed some boundaries and raised the bar for new super hero shows at the time. without shows like Batman Beyond then Young Justice might not be quite as great as it is today.
Speaking of surprises in Batman Beyond, I’m reminded of one of Bruce’s best lines to Terry:
“You didn’t have to kiss her.”