Honestly, I feel like the current iteration went too far; you're at the, "might as well start over again" stage with that low-frequency approach. I really like how you're attempting to apply Jansen's ideas- but don't forget how much emphasis he puts on form following function, too. That's something where in the designs where function is clear (like the tanker) it really works; where I think that things are harder is on some of the warships, where the functional concepts are not very clear.
But let's talk about the noise ratios first. For example, the gun positions, especially the front ones, look really vastly more noisy against the smooth plates, which I think is distracting and doesn't work well (I didn't think it worked well on the Tri-Tach stuff, either). That's a pretty easy fix; just reduce their noise a bit, work to the palette and smooth things out. But it's what I saw immediately and it pulls my eyes away from the main show.
But the biggest critique I'd give is that somewhere during this redesign, the new Eagle really lost its sense of scale. It no longer really feels like a big Cruiser, a massive, menacing wedge (with surprising maneuverability). The greebles helped, in the sense that they created a sense of function, even if they weren't really contributing much; when it's this smoothed out, the lack of functional meaning is clearer. A few areas of high-frequency, noisy detail or some functional areas in amongst those smooth surfaces could really help that.
The shuttle doesn't feel nearly so out-of-scale, because all that smoothness is compressed into a relatively small area, so it's not as obvious and the smooth is balanced. Even there, I feel like a panel line or two might get it to feel right.
There is also the major problem of losing the aesthetics that made each Faction distinctive, insofar as they've ever been differentiated; that high-frequency look was largely defining for early Independent / Midline ships, with their dull monotones, whereas Low Tech has always felt a little more organic and open and High Tech has always been smoother (well, other than a few outlier designs that look like they're alien tech).
This is one of SS's major areas where I still think it could be improved; visual themes that stay consistent across a Faction make them iconic and are helpful in terms of feel and as a marketing device.
I also thought that the comment about the Onslaught was interesting, in terms of understanding where you come from, design-wise. I've never felt that the Eagle was "related" to the Onslaught, visually (although that may have been true early on). They're both vaguely wedge-shaped, but none of their incarnations have really had much in common, design-wise. The Eagle and Falcon are clearly relatives, but bore more of a relationship with the Conquest, in most respects, both palette-wise and in terms of effect and specific patterns of greebles; the Onslaught's primary visual motif is that the big heights and overlapping armor plates, along with the bird-like rear section, give it a very organic feel, whereas the Eagle has always come across as a functional machine.
Anyhow, I apologize if any of this isn't what you wanted to read; figuring out what to transition and why is a very difficult choice sometimes when working on projects like this, especially where what you're doing as an artist and how you approach art has changed considerably over time.