I do indeed have game snaps too, but these only work partially too: 4:3 stuff looks fine but wider ratios like GBA/PSP don't look right in either square *or* horizontal-vertical since they're landscape rather than portrait.
I see, this happens because Arcadeflow expects snaps to be of arcade games, that's why it corrects the aspect ratio to show them in 4:3 or 3:4 (eg: CPS1 games have a pixel resolution that's not 4:3, but CRTs used in arcade are always 4:3, therefore the correction) .When a game is cropped to be square, it is again the 4:3 or 3:4 adjusted version that is cropped.
For console games intended to be viewed on TV screens it should be fine (as long as it can get the correct orientation, but his is an easy fix for me), while handhelds like GBA or PSP, that have a different aspect ratio, it will be stretched badly even in square mode. Moreover as I said the vertical or horizontal orientation of the game is not taken from the snap size, but from the game data (in the past I used the snap size but for some reason it was trickier so I went back to orientation data)
I'm not sure how motivated you are to make AF more compatible for console emulation, but it'd be so cool if you could add some functionality to work with more varied artwork/aspect ratios 
One issue is with the game data: I have no idea how to get all the game data for console games (I'm not that much into console emulation), but this can probably be fixed with a bit of study
Different aspect ratios... that's more tricky: the shadows effect under the snapshots are not "realtime": they are pre-rendered shadows in 4:3, 3:4 or square aspect ratios. So ther are two scenarios here:
1 - If you want to use box art instead of snapshots for the thumbs I'll need to make the shadows dynamic. And see how it copes with the game titles, and check how it interact with video thumbnails kick in. Of course a simplified version of the thumbnails grid with just game box art, no title artwork (unnecessary since there's the box art) and no overlay videos could be a solution.
2 - if you want to use screenshots as thumbs I'll just need to code something to disable the horizontal/vertical detection and the aspect ratio correction. Maybe there's a way to detect if a game list is Arcade or not...
I can't promise anything right now, but I'll think about it
