Interesting that the two Etymotics are different. They certainly do their best to confuse things.
I don't think you're going to find a lot of professional sound engineers paying much attention to these low-level consumer phones. A music professional would likely find both of them unlistenable.
From the specs, it looks like one is louder than the other to suit the modest amplification of some portable players. So you'd want to get the more sensitive one, the 6i, for minidisc.
If you can find frequency-response curves for both Shure and Etymotic--and I doubt you can, because the frequency response will depend on the shape of your ear and the companies can't figure that out for every ear--then you can see which one is flatter.
The flattest curve is technically better because it is reproducing the music more precisely. Without that kind of technical information, you are going to have to try them. Numbers are not going to give you the answer.
Look at these specs from Etymotic.
ER6
50 Hz - 6 kHz ± 3 dB;
20 Hz - 16 kHz ±6 dB
ER6i
50 Hz - 6 kHz ± 3 dB;
20 Hz - 16 kHz ±6 dB
What they are telling you is that in a middle range, 50Hz-6Hz, that the frequency response is almost flat, very accurate, within 3dB. Outside that range, below it and above it, there is more variation, within 6dB.
The bottom note of a piano is 27.5 Hz, so between 20 and 50 are some serious bass notes. And between 6 Hz and 16 Hz are the overtones that greatly shape the sound of instruments. Will you like the Etymotic's interpretation of those overtones? You have to try it.
The Etymotic specs say they ER6i are less accurate than the ER6. But maybe the tradeoff for volume is worth it, or the inaccuracies make music sound warmer.
Shure doesn't even provide that information, because each person will hear the phones differently.
If one were clearly better than the other for everybody, only one would have survived the market.
But read actorlife's post. He has a lot of headphones and doesn't use his Etymotics much because he doesn't think they have enough bass. I tried better Etymotics and also didn't hear full bass. There's a pattern here.
If you want to read a lot of debate on this try
http://www.head-fi.org and
http://www.ipodlounge.com . And some people will say the Etymotics are "clean" and "understated" and others will say they have weak bass. IEM's (in-ear monitors) are not the best headphones for bass to begin with. But in my experience, the Shures (E3 and E4--I haven't tried the E2) work better than the Etymotic 4P (I haven't tried the ER6).
If you look on eBay and have a little patience, you can probably find Shure E3 (gray) or E3c (white) for about $100. That's what I'd recommend.