Maybe it's the old school feel of the show's booking, or the shorter 1 hour timeslot, but I think Main Event is a better show than SmackDown for several reasons.
There are only 2-3 matches on this show every week, but they're almost always entertaining to watch. The first match of the night is the "main-event" itself, and usually gives us main-eventers and upper-carders going back-and-forth for 20-30 minutes. Sometimes theres a title match, which makes the show feel even more important. The second half of the show always features a smaller match for the undercard, but they're still given time to shine, which is something you won't see on Raw.
Michael Cole is a good play-by-play commentator, despite what some people think. The biggest problem he has on Raw is working alongside Jerry Lawler, who is a dull shell of what he used to be. Cole calls the action on this show down to the T, and dosen't normally change the subject mid-way through the match. The color commentary alternates between The Miz and JBL, who both work really well with Cole.
SmackDown these days feels like one giant re-run. If you didn't see a match from SmackDown earlier that week on Raw, you probably saw it the previous week on the same show. That's a problem for a show that is supposed to be it's own brand, complete with a world title. Main Event always feels like a breath of fresh air, with something different every week. It also has that ECW / NXT vibe of being in it's own mini-universe, which is a good thing.
All in all, Raw is obviously the #1 show by default, and I didn't know how Main Event was going to turn out when it debuted. But 5 months later, it's continued to exceed expectations, and in my book, is the true #2 show to watch right now.