He's not alone. I too liked just about everything but the CG and am glad to see I'm not the only one. Like the first series, the character animation and designs look great, absolutely great, but just doesn't blend well with the CGI at all. Gonzo very much kept the look of the old series, skipping the popular cel-shaded look (that they're usually bad at anyway so I approve) yet not really going too far in making it look like hand painted backgrounds like Macross Frontier, for example. It really looks like they animated it just after the first show, with a decades worth of CGI blending advancements all but ignored. It's somewhat better than before, but not like other, younger and supposedly lesser studios have done. They're not even all that detailed and the cloud layering in the beginning was pretty cheap looking.
It's at its worst with the Van Ships as you have outlined, handdrawn characters often clumsily composited into very smooth, somewhat paint shaded CG. The cockpits just plain stick out like sore thumbs. Especially when you first see it. Though the worst was Dio's roll; he looked pasted on. There's very little detail on some of these skins, and it barely matches the look of the tradition animation, so it just makes it look cheap. High end, yet still cheap. These are just above the look of the old Ps2 games Gonzo started on. Which is a shame, since they'd finally moved beyond that.
It's not the worst I've seen, far from it, but it's definitely no where near the best thing about the series and mostly seems there for the sake of being there. It was the key reason I couldn't really watch the first show, which I should love based on concept and Murata alone. Though I also attribute that to G4 airing it dubbed and not being able to separate Freeman from Alucard as well as all the lavish praise the look of the show got in Geneon's release. I though it far from "the most beautiful looking anime ever" splattered on the DVD cases. The hype machine killed it for me way back when. Though I shouldn't be having that problem here.
No one's crazy for not liking CGI in anime, by the way, no matter how well done you think it is. It's very much to personal tastes. I've pretty much hated CGI used for CGI's sake in shows from the get go, since it never blended. So I'm a bit harder than most, and it doesn't help that I can rarely appreciate the elements themselves (I've just never liked the look of it, nor though it "cool" like I do traditional and it doesn't help when it's screaming for attention). The CG in Blue Sub no 6 (as well as Hellsing though not for the CG) put Gonzo on my trash list for ages until Gankutsuou. Only recently have I mellowed about it and found myself able to tolerate it if used well enough in a good show. Unfortunately, thanks to Gonzo, we can't really get any mecha series without it these days, though great strides have been made in getting it to blend. Cel-shading is getting to a point where it no longer looks worst than simply going photo-real (or should I say "game-ish"), as evidenced by the minimally used, near seamless shots in Eva 2.22 (not the Angels, but the few Eva shots) and Gundam Unicorn; though I generally prefer the brush stroke look. Unfortunately, Fam doesn't really do either.
Still, I actually liked the characters a bit, and found it a bit easier to get into despite the ton of backplot dropped in it and some hectic pacing; so I'll give it a few more episodes at least. I want to like Last Exile, I really do. It's supposed to be Gonzo's serious masterpiece and reprieve from their usual garbage like Hellsing and Burst Angel. I just wish Gonzo would learn to stop taking such great designs and making it look like a video game. Though I suppose it's still better than their inconsistent animation in Speed Grapher and the two shows edited together that was the look of Vandread.
Man, I really haven't thoroughly posted true content here in ages. Good old AP.