I actually tried to re-read the series at one point, and even as a fan, I had to break things up. Read one WoT book, then one non-WoT book.
There's absolutely a storyline for the whole series. It's about the Dragon Reborn* preparing for the final battle against... basically Satan, who is about to break out of the prison he was put into thousands of years earlier and take over the world.
*Not trying to be pretentious there - I just don't want to ruin anything if you don't know which character that is yet.
Even after 11,000 pages, the series isn't quite over yet - there's one more book to go, scheduled to come out in about a year. Robert Jordan died a few years ago, but knew that he was going to die without finishing the series, so he took tons of notes, recorded hours and hours of sessions talking about what needed to happen, and picked someone to finish the remaining books. The new guy has done a really great job so far, though.
I've only read the first Sword of Truth book... so I'll leave the comparison to someone else. I prefer the Wheel of Time series, though.