First off, I've found that direct recording sounds one of two ways, electronic or overly processed. The PODs and
the Boss VF1 (which I love the effects for) sound good direct... but they also sound very overly processed. Most anything else sounds electronic.
If you are getting an electronic sound, one thing you can do is cut your highs. I suggest cutting everything above about 6k down to a minimum of -16db. A low pass filter with the 3db down point at 6k would work well also. That will get rid of that sawtooth harshness sound that your ME50 puts out. You then can tweak the crap out of the other EQ settings, but you won't get the signal "smooth" sounding like you hear on regular recordings (think Megadeth's Countdown to Extinction or Metallica's And Justice for All).
To make a long story short, I ended up just miking and recording that way. What I do is use two microphones, a Shure SM57 or Audix I5 on one speaker and an Electrovoice ND467 on the other speaker. I have both mikes sitting perpendicular to the face of the cabinet and about 1.5 to 2" off center from the speaker's center. They sit a thumb's thickness away from the front of the cab. I then run those each into one of the channels on
my ART TPS preamp to give it a good pre and some warmth, and then mix them down on a mixer about 50/50. I cut the highs on the SM57 and usually cut the lows just a tad on the Electrovoice. You can hear examples of this technique on my band's myspace site - Last Will from New Eagle, PA.
I know they've come a long way with the direct stuff, but it still just sounds very fake to me. One of the reasons that miking a real cab sounds so good is because you actually lose some detail through the speaker cone and again through the microphones. It basically smooths out some of the harshness that direct recording has. Also, a guitar speaker cabinet typically rolls off somewhere around 5k or 6k anyways, so you lose alot of that annoying ear piercing grit.
That's just my 2 cents.