+1 on eq. I use a rack eq and kill everything under 100 on my bass rig. No mud, but I still have punch. Unfortunately some sound men don't know that the frequency range under 100 causes the "mud," especially when the kick, bass, and guitar are putting out frequencies in this range at the same time.
A standard tuned guitar doesn't reproduce much of anything below 100Hz (100Hz is a little above the 3rd fret on the low E string. When I run sound (and just about anyone who can legitimately claim to be an audio engineer will put a HPF around 100Hz on a guitar. A common thing I hear from guitar players, is something like "I love how big and fat my guitar sounds with the bass turned all the way up." When playing by themselves, it may sound good, but in the context of a band, not so much. If you are having an issue with the guitar creating a lot of low end, try talking him into using a HPF and EQ his guitar so that there is more mid-range and high end. The band will sound better. As for cutting everything below 100Hz, I would advise against it. You're cutting out the fundamental on about 1/2 of your range!
Also, every tour EQ's the PA a lot, in an attempt to minimize reflections, but like elgecko said, arena's aren't designed for "good sound", even a .Wav file through the best PA won't sound like your headphones.
The other issue is that the sound is very different throughout the room, and there is only one engineer. Next time you go to an arena show, stand by the sound guy. It will usually sound pretty good.
If you're in the nosebleeds, like I am when I usually go to shows like this (actually, I'm usually backstage but still...), you'll predominantly hear bass. This is because, subwoofers are almost perfectly omnidirectional, which means there will be bass everywhere, whereas mid-range drivers and tweeters are directional, if you don't get a seat where the pa is aimed, it will sound bad. And even this isn't a guarantee. If you are too far from the stage, you will hear a lot reflections mixed in with the direct sound from the PA, making the sound undefined. This can also cause frequencies to be cancelled out, attenuated and boosted, which will change the sound.
Ultimately, it comes down to acoustics and money. There are probably ways of making arenas sound better (I have some ideas), but if a band can sell out an arena and make money doing it, why spend more than they have to. Trust me, the engineer knows about everything you're hearing. There are so many factors working against them that it isn't possible to fix everything and maintain their timeline (or make money...)