I own both, 100w has been my main amp since 2007 until I began playing a smaller weekly gig about a year ago in which I started using the 50w.
If had to sell one it would be the 50w. Just like the tone more of the 100w. However, it's from very early in 100w production and I don't think the later models sound as good. Could be the tubes. (not trying to start internet folklore). Also, the 100w sounds GREAT at low volumes so the 50w isn't needed for that reason.
Channel 2 is where the amp shines (both versions), ESPECIALLY in a band setting. I rarely use channel 3 now on either version. If you need more gain out of channel 2, increase the level of your boost or add another boost all together. Channel 2 is less saturated, more organic, and is tighter than channel 3. Increasing gain by boosting sounds better than increasing the amp's gain IMO.
The best sound with these amps IMO comes with the 100w, channel 2, through a Mesa 4x12 w/ V30's. Yes, I like it more than the EVH 4x12.
The ONLY reason I've been using the 50w over the 100w recently is due to the smaller size and I really like the tilt back system of the 2x12 with the head on top. Great for monitoring on stage. I use it as a side fill and never have to put myself in the monitor anymore.
For me, the resonance knob on the 50w has been useless. I set it to noon and haven't touched it since.
BTW, I've NEVER had ANY problems with EVH amps in the past 6 years of using them (besides one preamp tube that went bad in the 100w from bad outdoor power and a bad 100w footswitch cable).