I don't know you could you possibly think Lucifer I is more ominous and threatening than Lucifer II... This song tells you "This Lucifer guy is really fucking powerful and you shouldn't take him lightly". His second phase's music tells you "The Devil Himself is PISSED at you and you are going to get your ass TORN APART". The crazy percussion in the intro, the fear-inducing BWOOOOMs, the moments of quiet heartbeats and ambience... And my favorite part, in which the main synth begins playing the Chaos theme, but then the melody falls apart into an incoherent mess of notes, all while the percussion is going wild in the background. It's a very simple song; there's barely any melody or actual structure to the song. But it complements the mood extremely well. Lucifer I... is just a warm up to Lucifer II. Just like in the game.
I tend to like music the has some form of subtlety to it. Lucifer II is just way to obvious (and to me) is not that threatening it's more adrenaline pumping. This theme seems more sinister and (again) subtle. I guess i'm more used to Nocturne's version of Lucifer (calm and collected) which this theme does in a way represent. Though not to say his Lucifer II is not good it is, but as his boss it just doesn't work for me.
Here's the correct dialogue options if you need 'em. (Both are Neutral route though) Merkabah (1st Phase) Question: "For whom are you waging this pitiful battle?" Answer: "For the people of Tokyo." Result: Full HP/MP recovery Merkabah (2nd Phase) Question: "Merkabah gives Flynn a powerful and stern glare..." Answer: "Quietly accept it." Result: Full HP recovery, all stats increase greatly Lucifer (1st Phase) Question: "For whom are you fighting this relentless, dreadful battle?" Answer: "For the people of Tokyo." Result: Full HP/MP recovery Lucifer (2nd Phase) Question: "Lucifer gives Flynn a powerful and overbearing evil glare..." Answer: "Smile back" Result: Full MP recovery, all stats increase greatly