I posted about some issues on reddit, and I was directed here, so I'll just repost them:
- A lot of battle portaits have a one-pixel empty line at the bottom. It's noticeable on Roy in both 3.5 and the 3.6 trailer. Some also have it on the left border. It doesn't seem to show up on the portraits in Brawlbox. To easily see both lines, jump off the left side of Fountain of Dreams as black Roy. Might be fixable by moving the portait window's bottom vertices up and the left vertices right.
- Ivysaur's battle portait is out of place. There's a ton of white space at the bottom. Might be better if it looked like this: http://i.imgur.com/JzVZCpo.png
- A couple of alts (mostly the ones added in 3.5) use the default costume shadow models, but I'm sure that's already been fixed in 3.6.
- Retro Suit Samus' cannon cord texture is very dark, which makes the small details hard to see. Same goes for the darker parts of the shoulder pad underside texture.
- Melee Fox's eye highlight disappears under his left (relative to camera) eyelid in a few animations. Doesn't happen if you place the highlight where it was in Melee: http://i.imgur.com/foJWG9d.png | http://i.imgur.com/0stuGjO.png
- Speaking of Fox, his alt stock icon looks off to me: http://www.ssbwiki.com/images/c/cf/FoxHead64PM.png | Example fix: http://i.imgur.com/RWRRtBS.png
- Wolf's alt stock icon is just an edit of the default, even though the model's face is different. Guessing this has been fixed already like the shadow models. Wolf's shadow model is a poorly edited version of Fox's, but that's an issue from vBrawl.
- The ZSS alts have a lot of issues, but the biggest one is the lack of texture detail on the skin. She needs more defined elbows, knees, abs, etc.; otherwise, the costume looks flat. Also, a part of the alts' hair behind the ears is occluded by the bangs' transparency, but only on the left side of the head. (Again, relative to the camera.) There's traces of default ZSS' skin tone around the alt's eyebrows, too. I checked 3.6 Art Sunday to see if it was fixed, but the camera wasn't close enough to tell.
- Roy's elbows lack shape and definition compared to Marth's. Not a huge deal, though.
- This one is really a style choice, but the Melee Falco alt uses Brawl's eye texture, which is much brighter than the Melee eye. I think it looks better Melee style: http://i.imgur.com/HUjUKTM.png | http://i.imgur.com/k4f6Fin.png
- Sheik's CSP is kinda small. Especially noticeable when compared to Zelda's.
- There's this... thing on Smashville that extends from the edges. I can't tell what it is, but it looks like a pair of dark transparent rectangles. It's hard to see, but if you focus on the edges and jump around a bit, you'll notice. Not sure if it's in the netplay version.
- The Page 1/2 icon on the stage select screen loses it's highlight border if you switch pages, even if you're still hovering over it. This might be a vBrawl issue, though.
- Not really a bug, but with stock icons implemented, BPs are redundant. I know SSE uses them, but colors and series icons are probably enough with only two players max and cluttering the Versus UI just for SSE seems silly. Just some feedback, I guess.
Original reddit post with a few other issues brought up in the comments:
http://www.reddit.com/r/SSBPM/comments/3899k6/battle_portait_issues_and_other_visual_bugs/
Battle portraits: As you said, I'm assuming this is because of the model not fitting perfectly to the background
Ivysaur's BP: I'm pretty sure the Ivysaur BPs are from Brawl, I'm not sure if this counts as an issue. Do keep in mind that the Brawl HUD had names on the bottom, which is why the BPs are like that.
Shadow models: That's a massive amount of work for little payoff, if someone wants to make unique shadow models for all the costume that would be cool though.
Fox stock: I think it's fine, since it comes from the actual render. It shows more of his face this way too.
Wolf alt stock: I'm a bit 50/50 on the stock situation myself, ideally all the stocks would be in the same pose, or all the alts would have the poses from their renders.
Roy's elbows: Generally, the Roy model is very Melee styled, hence the proportional differences between other cast members like Marth.
Smashville thing: That sounds like the shadow? I'm not sure.
BPs: I've always thought BPs were a great addition, they make the HUD look much more modern. Removing them entirely would be a step back in the design department.
On things I haven't commented on, I don't have the P:M files on me so I can't reference. I do know that there are a ton of things being updated in 3.6 though.