Some things to consider in making your decision:
The Etymotics are tiny and lower-profile, and the Shures will seem huge by comparison (think of the relative difference between a sports car and an SUV). To generalize, the Etymotics might be an acquired taste -- something you have to get used to and grow into, while the E2s tend to be a "starter" IEM -- something you might grow out of if you keep reading these forums and spending more money.
The Etymotics will provide excellent isolation and lots of detail, and the Shures will have a lot of bass. (The ER6i is easier to drive and has more bass than the ER6. The ER6i comes in white or black.)
The earphone wires on the Shures are intended to loop up over the ear -- this helps secure the earphone in your ear, and it should cut down on the microphonics through the cords. The ultralight cords on the Etys aren't intended to loop over the ears; there would be some microphonics.
The Etymotics will seem neutral to trebly, while you might find the bassy sound of the Shures "fun" (or you might miss the highs -- depends on your preferences). The Ety's might sound "thin," to you, particulalry at first and on older recordings, but they convey a fair amount of bass on bass-heavy "modern" recordings. If you must have lots of bass, the Shures might be for you; if you must have clarity, the ER6i's might be for you.
The Etymotics will seem frail by comparison -- if you handle your gear carefully, shouldn't be an issue, though. (I find they make for a good minimalist set-up ... they're really light and small.) The Shures will certainly seem sturdier, but check past threads -- I've read some complaints about the build, particularly the cords. Both companies are supposed to have excellent customer service, so that's a good thing. I think Shure's warranty is longer.
Altec Lansing makes Etymotics-derived IEMs that cost a bit more than the ER6i's, but Head-Fi members have said some good things about them. Also, there's an increasing number of canal phone competitors to the E2s that you might look into, if you haven't already. Finally, the player you would use them with and the type of music you listen to would also be factors in making your decision.