I think what we have actually lost is twofold:
A neoclassical sound and neoclassical style chord changes on an individual instrument level.
Pinella's presence, or, more importantly, thickness in the mix.
I completely agree with this.
Underworld is definitely a step in the right direction following the "digitalness" of Iconoclast, but aside from the chorus of Underworld and a few solos here and there, there's not a whole lot of neoclassicalism going on. I will say, however, that almost every song on this album has a different feel to it, which is quite different from Iconoclast - orchestral (and too brief) intro, thrashy but catchy, brutally heavy but melodic, a power ballad, dark and even Gothic (at times), Eastern/old school Symphony X, mini-epic with Paradise Lost-ish sound, mid tempo with catchy chorus, 70s classic rock, a longer and more emotive and more keyboard-heavy power ballad, and Rush.
Charon in particular reminds me not only of V, but of tracks like Eye of Medusa, as well.
As for Pinnella, he is without a doubt more present in a "classic" sense on this album than he was on Iconoclast. Sure, he was all over songs like Bastards of the Machine and Electric Messiah, but futuristic synth isn't the reason I like Symphony X. What I'm not a fan of (and what is, unfortunately, still present on Underworld) is Pinnella doubling the guitar lines with a synth patch. That reminds me of Dream Theater, and says to me "We couldn't think of something unique for the keys to do here, so they'll just follow Romeo and LePond."
I miss the melodic piano lines that played over heavy riffs, like in Egypt, or Of Sins and Shadows, or Fallen, or Orion, or Eyes of Medusa, or hell, even STWOF. I think that sometimes they try to be too "metal," and as a result, they lose some of the sound that made them unique. Don't get me wrong - sometimes this is warranted. I couldn't imagine that 5/16 polymetric riff in the middle of Kiss of Fire with tinkling piano over it, for example. The same goes for that riff in the middle of To Hell and Back - it's too good of a riff on its own to have anything playing over it. But these are exceptions, and are few and far between.
As a whole, I think this album lacks some really memorable instrumental sections that don't feature solos. Their older material had tons of this - hell, even more recent tracks like Walls of Babylon and Iconoclast featured this style. But this album, in my opinion, cuts to the chase too quickly. If I want songs where the vocals enter 10 seconds in, I'll listen to the radio (I don't ever want songs like that).
But, to reiterate - I do think this album is a step in the right direction, especially with the diversity of the songs. And, while some may disagree, I like the mix. All instruments can be heard clearly (with the infrequent exception of the keys), the album isn't too loud (Paradise Lost), and the bass tone is silky, smooth, creamy, and vibrant (unlike Iconoclast, where it was buried).