For those who have used it, have you experienced any problems connecting to the 1/4" TRS inputs? I've read in here (and elsewhere) that this is a problem. How serious of a problem is this?

It's a serious problem. The Microtrack II preamps are not very clean. Making it worse is that the gain controls are digital - changing the gain just reduces your dynamic range. This makes the phantom power feature worthless. You really need a preamp/mixer with gain and phantom power upstream.

When operating the Microtrack II, set the gain at 50% and never, ever touch it.

In addition to preamp noise, there is some repeating pattern noise. It's not terrible, but it's not world class either. If you have a strong signal, it's ENG quality, but certainly not Hollywood feature quality, IMHO.

You can hear it for yourself in the following review. In addition to the video, there is a link to the uncompressed audio: 5. Canon 5D Mark II Audio Exposed - Noise on Vimeo (http://vimeo.com/5474562)

That's really too bad, although I can't imagine a situation where I wouldn't have a preamp in front of it. I also really like that it has an S/PDIF input. Are there any other recorders in this price range that also feature this? I do have an excellent AD converter I would use with it most of the time.

...I can't imagine a situation where I wouldn't have a preamp in front of it...

When we bought ours (fortunately at a very low price for a clean unit with the box and all the goodies through craigslist), we specifically chose it because of the balanced inputs and phantom power. Oh well. The phantom power turns out not to be useful, and the noise is higher than anybody would expect from balanced inputs.

Using the juicedLink CS231 as a front end makes the Microtrack II usable, but it's still not as clean as the H4n or the JL/5D2/MagicLantern combo.