I was trying to choose between Shure and Etymotic recently and found myself simiilarly conflicted. Ultimately I chose Shure (and I'm very happy)--here's why.
First off, a comparison between the e2c and the ER6/ER6i is unfair. At this point, if you go on Amazon, you'll see that the e3c is priced to compete with the ER6, and while I've never heard the e2c, I've gotten the distinct impression that it is considerably worse than its bigger brother, so I'd recommend comparing the e3c and the ER6i
Second, while the difference between the e3 and the e3c is purely cosmetic (c version has white buds to match iPods), the difference between the ER6i and the ER6 is substantive. The "i" version has far less impedence, so that an iPod is able to power the headphones without an extra amp, which is what most portable users want. This creates the impression of having more bass, though properly powered, the higher impedence ER6 (or the e3c for that matter), should have at least as much bass.
This leads me to what I think is the most important question: What do you want these for? If you're shopping for great headphones to sit in your living room with a good source and amp, then get the ER6. However, they'll sound pretty bad just plugged into an iPod because they'll be underpowered. I've found that the e3c is a good compromise on this issue, because they sound good when I'm walking around (and usually am not too critically focusing on the music, which is compressed anyhow), but sounds considerably better on a bus ride when I can throw a portable amp into the mix. I've seen a lot of people complain about the e3c's bass, but they haven't tried plugging it into a portable amp--it makes a big difference on the low end. (btw, as far as high end goes, the e3c takes abotu 20 hours for the high end to "break-in", give them a chance).
If like me, you're looking for portable earphones to complement a bulkier at-home setup, then I think you should consider the durability factor. The Shures have a very tough build with thick wires, a great 2 year warranty (contrasted with 90 days for etymotic) and a neat case. Etymotics have skinny little wires like the cheap sonys. Doesn't mean they don't sound great, but broken headphones don't sound like much at all. Shures and Etymotics both sound good, but if you're looking for portable earphones, then consider whether your criteria should be the same as for at-home headphones. I've been very happy with the Shures, hope I've been helpful.
Good luck!