Eric is dead on, it really is personal preference. I know everytime I used the stock SL2 with the guys, I was always amazed at how fat and mean it could sound, yet smooth and could sing a baby to sleep. I changed it to the X version but have yet to really give it a whirl with the band.
In my opinion, Egnater's version is a better version of a Marshall which is why I liked it better than any Marshall I have owned. I think in stock form it has plenty of growl and punch and I don't notice a lack of clarity. With the X factor, the big difference to me is that it has more sizzle and hair, which is not necessarily my thing. Nothing wrong with that, just my preference. I never felt like I needed more bite.