It really depends on which branch of the El you're on and what time of day. The north, northwest and southwest branches (Purple, Brown and Orange lines) are reasonably clean and moderately quick (they have fewer stops) but get ridiculously, Asia-level crowded during the rush. If you are at the edge of one of them (and can thus get a seat), it's not bad.
The north/south (Red) and cross-town lines (Blue and Green) are dirtier, slower and less safe. Part of that is just the realities of the neighborhoods they go through, but they also have a lot more stops, so there's a lot of jostling, bumping and standing.
The El also can have some fairly aggressive panhandling and muggings. The CTA, in general, is much more laissez faire about such things - partly because they got rid of the conductors that used to patrol the trains, partly because it's politically toxic to roust "undesirables" from public transit. The Metra (diesel trains) still has conductors who police the train (the Metra uses an on-train ticketing system, so someone has to be onboard), so the ride is a lot safer and civil. The Metra even has "quiet cars" where talking on cell phones (or other passengers) is prohibited. That's a nice ride.
I rode the El daily for 10 years and the Metra for 12, so I've seen the best and worst of both. I've specifically chosen where I've lived based on convenience to public transit - in my adult life, I've never lived more than three blocks from a train station. Due to a serious injury, I've recently had to switch to driving and while I've gotten used to it (there are a few upsides to being alone in a vehicle), I'll never get used to the boredom and waste of driving a vehicle into the city on a regular basis.