I never played the original SNES version, but from what I've played of the remake (a fair while ago), I prefer it to the SEGA version.

The SEGA version wasn't a bad game, but it was grindy AF. What made it even more grindy was the fact that it was very easy to permanently lose all your (really expensive) software in the matrix. Which is why I never got very far into it.

I think the Shadowrun Unlimited UGC took a lot of inspiration from the SEGA version. Unfortunately SR UL isn't being worked on anymore, although the author did release the source and assets of the module so others could build on it. It was actually shaping up really well - and the way SR UL did the matrix was really good (i.e. you can actually use skills/programs in the matrix properly, it has a "matrix-like" design to it, it didn't have retarded real-time aspects like the HK matrix, etc.). It also changed all the weapons so the accuracy was far less, which I thought was a good approach. The only thing it needed was a better fleshed-out plot - it mainly had repeatable (and repetitive) runs from what I recall.

Edit: It appears the SR UL author has decided to continue work on SR UL after all! Last update was August 2017. It has 35+ runs now. I'd recommend it to anyone who liked the SEGA version in particular. Link: https://steamcommunity.com/sharedfiles/filedetails/?id=453526979