I've gone both ways (Metra and L) dozens of times. Metra has to fit your schedule, but when it does, it is far and away the better choice.

Advantages of Metra:

* FAR more comfortable... you can actually get a seat with some room (exceptions possible if it's the Friday afternoon of a three-day weekend) and if you're a few minutes early you can usually get a seat on the upperdeck
* Better clientele than the L
* Train leaves when the schedule says it does
* Train arrives at the O'Hare Transfer station when the schedule says it does, mostly
* Fewer delays due to track work or the million other things that disrupt L trains. I never missed a flight due to a delay on Metra, but came close a few times due to the L, and know people who did miss flights due to delays on the L.
* The Metra/bus/peoplemover interface is far more efficient and reliable than it may at first seem
* You don't need exact change to buy a ticket
* 10-ride tickets are still discounted, whereas CTA got rid of most of its multi-ride discounts a couple years ago
* Slightly more scenic than the L -- not by a lot, but anything's better than the median of the Kennedy.

Disadvantages of Metra:

* Slightly more expensive than L (about $1/ride)
* Schedule is far more limited than L -- generally following weekday commuting patterns into and out of downtown
* Have to buy a ticket the old-fashioned way, by waiting in line and asking a human being at a counter, or on the train (if coming from ORD). Lines get long around the end of the month with people buying new monthly passes.
* Fewer trains means greater consequences when you miss one
* Going out to ORD, you have to make sure you get on the right Metra train and don't miss your stop. I have almost made both mistakes. On the L the former is hard to do and the latter is impossible to do.
* Harder to time when going fom ORD to downtown, due to unpredictability of flight arrivals etc. Also, you get on relatively close to the end of the line, so trains are usually pretty full.

Metra works best when you are going out to ORD, are already in the vicinity of Union Station (note Union has a less obvious entrance on Madison Street, diagonally across from the Olgilvie Station) and are leaving downtown around afternoon rush hour. I found overall travel time (accounting for the train/bus/peoplemover xfer on Metra) to be pretty much a wash in ideal conditions. Which occur much more often on Metra than on CTA.