Mmm, never thought about that before. I think bottom version might be more common, though I can't back that up with anything. It's the one I've seen most when looking through PS1 games while shopping. The other looks a lot similar to the GTA 1 cover. I thought it was a the same picture when I first looked at it. Looks like the same scene just at a different point of view. A little of topic, but if you are interested in the orignal GTA games check out Edge Issue 164, they had a great article on the development of the first title.
I think the second game cover was redesigned because it caused confusion due to its similarity to the original game's design.
That first design is a perfect example of complacency, which isn't a word I'd ever associate with Rockstar (sarcasm)...
