One of the things I notice frequently when recording bands is the kick/bass guitar alignment (or more commonly, misalignment.) I realize that during practice, it's often hard to hear what the drummer is doing on the kick, and it's equally hard for the drummer to hear what the bass player has in mind. But, to make a tight, professional-sounding recording, it's important that they know what each other is doing. I often hear, upon playback of a first take, "Oh! I had no idea you were playing that! That totally changes what I should be doing!" And while it's nice to be a witness to such revelations, it'd be more cost-effective for the band to work these things out in advance.
Bass players are often former guitarists, and approach their instruments as "the low-end of the guitars," which is definitely a part of their function. But, as a part of the rhythm section, they are also an extension of the drums. The best bass players realize this, and are very much aware of what the drummer is doing, and vice versa.
If you ever see the Pixies live, you'll notice that Kim Deal stands right next to David Lovering, and they make frequent eye contact, almost oblivious to the rest of the band. They lay down a solid, tight line, that anchors the wanderings of the others.
You have to think about it like it's one instrument. If the kick is hitting in a certain pattern, the bass should work with that. Play at the same moments, or in between, but in a way that works together. A bassist banging away on 8th notes all the time will often sound wrong, no matter what Van Halen might have done.
So that's my rant for today. Bass players and drummers should practice together, without the rest of the band. Record your rehearsals, pay close attention to what the others are playing. But mostly, ask your self whether your bass line is working with the drums. Do you know the kick pattern? Do you know where the fills are, and how they are counted? Learn it, figure out EXACTLY what is going on.
You'll be much happier with the recorded results, and your live show will benefit tremendously, as well.