I think I'd take a little issue with the shapes that the #3 eagle suggests, before anything on the new design. The oval-like shapes feel a little tacked on.
Meaning it still kinda looks greebly.
But removing the greebles is still nice- I think the issue with a lot of ship design is more visible between, say, the old star wars trilogy and the prequel trilogy.
A lot of the initial trilogy's ships had greebles and uneven surfaces and looked far too busy, with cannons for, say, the death star being boxes tacked ontop of an extremely greebly landscape- so they vanished into it.
On the other hand, the clone cruisers, specifically the carriers featured in the prequel trilogy.. are a lot more smooth, and they have contrast colours.
The turrets are generally in even spaces along the surface/top side. With the bridge/shield generator elevated. They're mostly white exceft for the hangar bay door which slides open being highlighted in red.
It's simple, it's just greebly enough to draw attention and it's mostly smooth and you see clearly when the hangar bays open.
So it's a step in the right direction but from your own words tacking on the little half-shapes kind of retains a greeblyness that I, personally, don't think should be there considering most of the ship is so angular/straightened vectors. Two of the forward guns on the newest eagle look a bit tacked on compared to previously- Like they've been glued into place on a model after it's been finished like some kind of afterthought.
On the other hand it's a lot easier to see what the ship is, what it does, what guns point where when mounted- so it's a good progression even if it might not suit everyone's taste. On the upside of this, the ship also now looks like a complete piece where the hull itself is concerned, the middle forward section no longer looks as out of place as it might have.
Other than that I have no complaints- this could be a very good thing especially for a few of the phase ships out there because some of the larger ones I find I have problems seeing the turrets on, for instance.
The apogee could possibly also use some streamlining. For a supposedly high-tech ship it looks somewhat greebly compared to the other ones.
Keep up the good work!