The 001 isn't very comfortable, true. The main problem is that there is a lot of pressure that's applied to two small earpads resting on the ear canal (when the system is used with the headband). The solution is to bend the headband outwards to reduce the pressure. This won't make them comfortable, but it will make them a lot less uncomfortable. There are also different size pads available, and bigger pads are usually more comfortable, but in my experience, they reduce the amount of bass.
There is some treble roll-off, and it is contributed to by both the headphones and the amp. Today I just got my SR-003, which I'm using with the SRM-313. While it's still not burned in, I can finally pinpoint the deficiencies in the SRM-001, and there are plenty. It rolls off the treble, restricts dynamic range, and in general sounds mushy and a bit unresolved. The SRM-313/SR-003 combo sounds crisp and punchy, yet still retains the SR-003's warm tonal balance. Treble is a lot more extended than the SRM-001, as is the bass, but treble extension is still lacking, especially next to the SR-404. Out of an AC adapter, the SRM-001 improves considerably, however, and is a lot closer to the SRM-313 than under battery power. It becomes a lot more open and dynamic, and extension improves on both ends. But, there is some background AC hum, and the sound is still not as punchy, open, or dynamic as the SRM-313.
Anyway, this is all really out of perspective, since we're comparing a battery-powered $100 amp to a full-time class-A $500 amplifier. The SRM-001 doesn't sound that great under battery power, but the whole system still sounds good, especially for a portable. Under AC power, it can get close to a full-size amp, but of course it doesn't go all the way.
If you want advice on what to get - SR-60 or SR-001: if your intended use is portable and with an mp3 player, the SR-60 would be better. If your intended use is stationary out of a good source, then the SR-005a system would probably be better. If you need something that can be used both portably and transportably/stationarily, then the SR-001 is what you need.