I enjoy both these shows. They play side by side on the MeTV Network. I've noticed though, that beside maybe the whole quality of special effects thing, I don't see a whole lot of differences in the 2 shows.
They both utilized the earthly similarities on alien planets. Just like Lost In Space, the Star Trek producers found excuses for the crew to end up in Nazi Germany, Ancient Rome, confronting a Greek God, a shoot out at the OK Corral, etc*.
Which one wins out? That's a tough one. I got to say though, at least Lost In Space had Dr. Zachary Smith.
* Fortunately, and I think this is mainly due to the timing of the original series, there was no exorcism scene like there was in The Next Generation series.
Well, one had topical shows, a steller cast, great guest stars, REAL Sci-Fi writers and no kid actors as regulars.