I've never played Subwar 2050, but I'm a huge fan of I-War, so I strongly suspect I'd enjoy this earlier Particle Systems game as well; it would be good to hear from other fans, though!

How do they compare?

Subwar plays more like a sim than an action game in that it is comparable to I-War.
It is not comparble in storytelling, Subwar is told in mission briefings only but it gets the atmosphere right which is important.
Other than that it is a much older game so expect lowres graphics, still very nice for its time and it has good music and sound effects.
I found the weapons in subwar underpowered though and it makes the game unnecessary difficult imo.

I actually wanted to play Subwar 2050 before starting with I-War some days ago. I was really surprised by the atmosphere that Subwar creates and soon learned that the game is much more a simulation than, say, Schleichfahrt (Archimedean Dynasty) was. You can be very methodical in the game, and it kinda reminded me of how I play Ghost Recon.

On the other hand, I don't think it did age all too well. You'll have to accept the low res graphics. In the first System Shock I had no problem with that, but in Subwar (where the screen is arguably less cluttered) I found it to be a problem for some unknown reason. You will probably simply have to try.

Besides the graphics I found the joystick control off. My stick has very small dead zones, but in the game I had to move a lot before the boat started moving. When I switched to keyboard control for comparison I actually found that to be much smoother.. though I am not sure if that is a problem with the game or simply my joystick.

My advice to you, or anyone else stumbling on this thread: if you actually are interested in playing a game that old, then you are probably a bit older and a seasoned gamer. If so, then the price on gog is worth the gamble.