Let's take a listen to a comparison featuring The Clash's "Train In Vain" recorded off a nice original UK pressing:
I'll cut to the chase here. I can't hear much difference between these carts on this track. There is a slight difference in channel balance with the Shure leaning a little more toward the left channel and the AT to the right. That's about it. I'm not saying there's no difference, only that I can't hear it. Maybe you can.
Looking at the frequency response graph I created shows that indeed the two carts share a similar tonal balance. The AT-95E has a bit more energy beyond 6 kHz, but other than that they look (and sound) very similar.
Both the Shure and the Audio Technica performed well on the bias tracks of the Hi-Fi News Test Record, with the AT playing all four tracks without distorting, and the Shure only breaking up slightly on the final "torture" track. I don't particularly hear any problems with their tracking ability on this famous inner groove track. The Audio Technica measured slightly better in terms of channel separation, and its channel balance was a little better too at +1 dB in the right channel, where the Shure was +1.5 dB in the left on the pink noise track.
One thing to note: The Shure M97xE was outfitted with an LPGear Elliptical stylus, not the stock Shure stylus. If you want to hear the difference between these two styli, listen here. It's not substantial, but to whatever degree I hear a difference it favors the aftermarket LP Gear stylus.
I've bought two separate Shure M97xE carts and both had issues with the stock stylus. The venerable cartridge maker in my experience really let quality control slip over the years. With rivals like Audio Technica offering a $50 cartridge that easily competes with what was at the time their top-of-the-line cart, it's not hard to understand why Shure chose to get out of the cartridge game altogether. Despite their history as innovators in the world of cartridge design, they seem to have given up years before they officially closed their phono production line.
If I sound down on the Shure, I don't mean to. The M97xE a nice sounding cart that can be made even nicer sounding with various exotic aftermarket styli (including the Jico SAS which really transforms the sound the cart), but I can't recommend going out and paying some of the crazy prices people appear to me asking for them right now when you can arguably get something just as good or better for $50.
There are other competitors in this price range including the Ortofon 2M Red which I've not heard. Next we'll hear how a Nagaoka MP-110 stacks up against the AT-95E.