I got about halfway through the first one and, though I liked it, I found the levels to be a little long, and a little repetetive (probably what made them seem long). I found each level could have had at least one full board taken out of it with no change to story or gameplay, sometimes more.
How is the second one in that regard?
Also, will I be missing something story-wise if I just skip the rest of the first one and go right to the second?
Some of the levels are a bit long, yes, but you gain a power early on to 'port' back to your home base (but only usable every 5 minutes), and from there you can save your game, thus allowing you to play the game in short bursts at a time if you so pleased.
Story wise, not really. The only thing that connects the first game to the second is a short movie right before the end credits of the first title. Beyond that, they're stand alone.