They're about equal. Both terrific.
The second is a lot more well known, probably because of the ancient graphics and archaic control scheme found in the first.

I just started playing SS1 again on the CD (only had played the floppies many years ago).
I didn't realize the CD had Voice acting, which would have probably lessened my surprise when I first played SS2 and discovered they had changed SHODAN to be female. I had alway imagined SHODAN having a Hal/Xerxes voice (probably adding to my surprise/confusion in SS2). Oddly the logs still say "him", but the voice actors say "her"
If I remember correctly, SS1's controls were pretty much the same as Arena/Daggerfall, especially concerning the mouse. I think the jarring thing of the interface is that for us, looking back at it, it was "SO CLOSE" to the WASD controls of today, its easy to default to WASD in a panic and then you die because W does not move you forward - bah!
melchiz-
They are both great games. That said, they are very different in terms of gameplay. If you've played Bioshock, that is the spiritual sequel to SS2, and you will find them similar in many ways. SS2 is a little more RPG influenced with inventory management, skills, etc. When it came out, many loved the atmosphere and it was a "scary" game. It's 10 years old and the graphics reflect that, so what was once scary may now be a little cheesy...
SS1 is very different in game play and reflect a different gaming mindset. Its not as twitch based as shooters today are. The "puzzles" are real puzzles, and there are some really creepy moments (the death cut scene when you are assimilated - the look on your face --shudder). The bad guy, SHODAN, is considered to be a top villain of all time. Also note, 15 years old, 2.5D. Things like the concept of having a bridge in game and being able to walk on top and under it was a big deal back then ;-)
Try them you'll love them.
ps - anyone have a good way to take out a hopper in lvl2? I used most of my magpulse on the sec-1 (2 shots left), and I'm not getting enough battery drops to really keep using the sparq beam.
pps - also just realized the Crusader reference from the intro cutscene. Is SS1 set before or after Crusader?

The references are just there because they were both published by Origin. Some document included with No Remorse (IIRC), mentions SHODAN. However, they are not in the same universe.
As for the hoppers. try some grenades if you have any. You can throw accurately by clicking and dragging before releasing the mouse button. The distance and angle of the drag affect the speed and trajectory of the thrown object. Practice throwing normal items, or non-live grenades first.

I have actually never taken him in any other way than using a grenade

See, I remember seeing some document as well, a time line, that seemed to indicate Crusader, SS, and, centuries later, Wing Commander were all different time periods in the same universe. Thing is, I can't remember when or where I saw such a document. It must have been fan-fic or something similar then, oh well.
The Origin thing makes sense, especially considering the same people probably worked on different projects.
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Never thought of a gernade! haha! usually its 8-10 hits with the sparq, which annoys me and it been so long since I last played the game, I've forgotten most of it, like writing down the number from the nodes - at least it'll give me a reason to go back to medical level; I can even try to get that last 1% of security knocked off :-)