Primarily, it was due to the changes in technology. WC1/2 (also Academy and Priv/RF) were done as a series of pre-rendered bitmaps of the ships at various angles (why the images would sometimes "stutter", particularly in Priv/RF, as it couldn't decide which of two angles to show the viewer). From Armada and onwards, the ships were rendered on the fly (*ahem*), and for the systems at the time (486/66 was a pretty decent machine, at that point) it was prohibitively expensive, in computational power, to do those renderings on ships with lots of curves, as on the WC1/2 ships, and still have the game play decently, so the ship designs went to simplified, angular shapes that weren't as hard on resources.
(This may be idle speculation, but the 2v2 limit on Armada might have been a decision to keep systems from puking when trying to render the relatively complex curved shapes of the 2 Academy (WC2 style, remember) ships that came over to Armada, the Jrathek and Wraith. That's just semi-educated guesswork on my part, though. I could be wrong.)