So... a goofy song about a girl from China complements a scenario where you're helping two policemen fight off space robots?
I admit that I don't know what they're saying in every song so I can't say for sure if the music really complements any of the scenarios, but to me all the song choices seem equally as random as Ouendan as it does in EBA, save for the "sentimental" songs (Over the Distance on Ouendan and You're the Inspiration on EBA). Whether a song "fits" the scenario doesn't really affect my enjoyment of the game in either direction.
I'm probably biased because I played EBA first, but I honestly do feel that it's the better game. The extra features make a big difference to me - it's annoying not being able to see what my high score for a song is from the song select on Ouendan, plus you don't even get to see what the full notecount breakdown was for your high score (it's more important for me to be able to see how many 100's I got on a song to be able to judge how much I could improve it). And being unable to skip the song intros... three words, Ready Steady Go. Ugh.
Also I think the biggest argument against Ouendan being a "more realized" game than EBA is that a lot of its note patterns are a lot more erratic. This isn't a big deal until you get to the highest difficulty level where you have less time to react - there is no easy segueway into the highest difficulty, because the first song is making you hit successive notes on completely different sides of the screen. It's very hard to react to something like that, you practically have to memorize the patterns just to have any chance of doing well on the first stage. By contrast, playing Walkie Talkie Man on Hard Rock is nowhere near as difficult since the patterns are simple and don't stray too far around the screen. Sure it gets more difficult later, but the difficulty curve for this was implemented much better in EBA.
I can understand people preferring Ouendan because they played that first and they're more familiar with that game. But I swear I once saw someone say that they preferred Ouendan to EBA purely because they had no idea what was going on in the songs and scenarios in Ouendan, that knowing everything about what's going on isn't as fun...?!?