The albums with Neil Morse are most definitely better. I wouldn't bother with the later stuff.
For me, the best two albums are, by far, Day For Night and V. Day For Night has classics like the title cut, Skin, and The Distance To The Sun, while V has At The End Of The Day (probably my favorite track) and the massive epic The Great Nothing.
I'd go with one of those two albums first. They also did an interesting double concept album called Snow (the last one with Morse), but it's a bit uneven and meanders pointlessly in places. Beautiful packaging, though.