Well, since my name has been invoked here, I'll chime in. The biggest factor in tone is the player, so I would suggest spending your money (and time) on finding something that is clean, relatively lightweight (which Bag End is not) and relatively inexpensive. Lots of good suggestions in this thread for items from Mesa, Bergantino, etc. Phil is even using Hartke a fair amount these days, which I initially found kind of horrifying since my experience with the brand has been pretty negative, but again, the single biggest factor is the player. So get a decent working rig, practice a bunch, work on your interplay with the band, and then keep your eyes out on CL, etc., for an Alembic pre at great price. Another option along those lines is the SMS CTP. I have one (actually, the first demo before production started) and it does what one channel of an Alembic F-2B does at a lower cost and with a few more options. Plus, Brad will build it to suit your tonal goals, if you talk with him. [Invalid or Expired Link Removed]
It's a great preamp! But, as also noted, there are many other preamps that use the same tone stack.
As far as versatility of the tone controls go, that's a different discussion. In my view, the Fender stack isn't meant to be versatile in the same way a parametric is. It's meant for coloring and broadly shaping the tone. It does that very well. If you need a more surgical eq, there are plenty of options out there (Phil uses a Meyer CP-10, which can be found pretty cheaply, just make sure it's the model that will correctly interface with a bass rig). My philosophy is that if I need that kind of surgical EQ, there's generally some other problem for which I'm trying to compensate, so I try to fix it at the source. One of the benefits of playing through a good in ear system, is that you get to hear a much more accurate representation of what the bass sounds like going to the FOH than just about any bass speaker cabinet will give you. Colored cabs like the Bag End bass cabs can give you a pleasing sound on stage, if you like what they do, but it will probably bear little resemblance to what your bass sounds like out front after going through the PA (and the ears of the sound person). Consequently, I've tried to get bass cabinets that are flat sounding, which have included fEARful cabs and now I play through a Mike Arnopol Soundworks Flex 210.
If you are going for a tone based on what Phil goes for, the only thing I would say is to avoid Ampeg and other brands that emulate the Ampeg tone (such as Markbass). While Ampeg does what it does brilliantly, it's generally a very colored sound and doesn't get totally clean.
All that said, my favorite Bag End cabinet is a Bag End II single 15. They haven't been made in decades and mine is held together with Bondo or some other nonsense a previous owner applied to it, but with a JBL K140 it sounds really nice, it's very light, and puts out quite a bit of sound without blowing up. I've been looking for another for a long time, but they seem to be very rare.
In general, my power amp is a Quilter Bass Block. 800 watts in a ridiculously small and light package and if I need to, it works well as a stand alone head. I'm using either a Groove Tubes Studio Bass preamp or Alembic F-2B. Both sound great and it's interesting that despite the very different topologies, I still sound pretty much the same through both of them. Which brings me back to my original point....