The problem is that those flaws are CLEARLY visible to me while playing the game. As I said, I had not actually seen a screenshot of that area until after playing the game (media blockout on purpose).
Regarding the color scheme, that is one area that I was truly impressed with (more so than even with the Saturn titles). I did notice that a lot of alpha effects have pretty serious dithering, though (like JSRF). The filter used during cutscenes, the darkened clouds during the first boss fight, and other similar effects all appear very grainy (especially in dark scenes). Not a huge deal, though.
I'm not trying to say the game looks bad (it absolutely does not), it is just incredibly uneven. That's what prevents it really impressing me...
Some of those games easily have roughness comparable to any in Panzer Dragoon Orta without accomplishing a lot of what it's doing
Many of them do have flaws, but those flaws are very different and do not bother me in the same way.
I can list the flaws of each game that bothered me (I enjoy doing these)...
Metroid Prime - This was almost flawless in terms of visual presentation. It faltered in one area, however, and that is water and other similar effects. The pools of water were very simple and simply were unattractive in comparison to the rest of the game.
Outrun 2 - I have only played this at the arcade, and quite frankly, I see absolutely no visual flaws in the game.
Ninja Gaiden - I can't really find fault with NG either (outside of VERY minor issues, such as the occasional bit of tearing).
ZOE2 - Suffers from some pretty heavy slowdown in several scenarios. The massive 1000 enemy fight, for example, ran very slowly most of the time...
MGS2 - The textures look good in game, but are rather low resolution and the game has a few issues with tearing.
MGS 3 - Based on the demo, it only runs at 30 fps and has slowdown issues.
ICO - Runs in low resolution, at 30 fps, and uses plenty of low resolution textures. Also, it cannot be forced to run in progressive scan.
REZ - Nothing particularly wrong here.
Silent Hill 3 - Per-vertex flashlight beam on PS2 and only 30 fps. The PC version solves both of these problems, though.
Biohazard 4 - Can't really judge yet, but it looks great.
Burnout 3 - Lots of little flaws throughout, but nothing major.
Wreckless XB - Uneven framerate
Panzer Orta has a flawless framerate, incredible creature/structure modeling, and a brilliant art design...but the flaws I've mentioned always stood out like a sore thumb. Even though Orta sports a higher level of detail than many of those games I listed, I believe the resources could have been put to better use.