Pegasus spontaneously sprouts an extra turret mid battle.... Even New Caprica when compared to prior work shows a dramatic drop in overall quality. While NC has lots of showy crap going on like the atmo jump and the Pegasus ramming if you actually compare the details between the zoic's work and inhouse you can see it easily.
"Exodus" was the last episode before they went totally in-house. It was done by Atmosphere VFX, who also did a lot of Centurion work in season two and "The Hand of God," among other shots spread around throughout the first two seasons. It's hard to get an exact itemization, especially in episodes where multiple companies may have contributed shots. For instance, Atmosphere got an Emmy nomination for "Resurrection Ship, Part 1," but does that mean they did the whole thing? I don't know. There aren't any shots from it in their reel, nor in the portfolio of an artist I know who works there.
My point is, let's not start fetishizing the first half of the show. It's not like Zoic or Atmosphere never screwed anything up. I can think of three shots off the top of my head there were obviously roughs that never should've made it to air. One of theme was a stock shot used several times before, so the use of an unfinished version was totally inexcusable. There were also a few cases of pieces of battlestars missing in certain shots. Maybe Pegasus's extra turret was to make up for its missing flight-pod struts.
Or the fact that it didn't get a flight deck until "Razor" (remember the really tight camera work on the Vipers landing in "The Captain's Hand"?).
As for the Babylon 5-ification of space in the latter half of the series, I'm not sure how much of that you can blame on the actual artists. For one thing, there were a lot more motivated appearances of weird space stuff. The New Caprica nebula, the Lion's Head nebula, the star cluster, the Eye of Jupiter nova, the Ionian Nebula, the trinary star system, and the black hole were all written in the scripts. While there were other instances of colored space just for the hell of it (though they were sometimes also motivated, like to visually differentiate different areas of space, as when Boomer was jumping to the Colony or when Gaeta was lost in his Raptor), I'd say at least half, possibly more, were the writers' doing. Also, let's not forget that the first two seasons weren't exactly 2001. The miniseries had Ragnar, and didn't even bother to say (or clearly depict) if it was a planet or just a negative space wedgie. Then there's the "Hand of God" asteroid thicket, the "Home" asteroid thicket, the "Scar" asteroid thicket, the "Hand of God" dust cloud, and the New Caprica nebula.
There were also a couple of shots in "The Plan" that perfectly matched the first season aesthetic, so the change in style was definitely a deliberate choice and not a case of incompetence or inability.