Hi Clyde -
There are a variety of answers to that, and it really depends on the goals of your particular group.
Good bit of reading you can do here:
www.ptotoday.com/ptovpta.html
As you noted the financial piece can be big. The average PTA unit pays about $1000 per year to remain affiliated. Whether that' a lot or a little, to me, depends on: 1) how many unique PTA resources you're taking advantage of; 2) whether those resources are available elsewhere; and 3) the size of your group's budget. If you're a $50,000/year group than perhaps $1,000 isn't all that much.
Some other differences I'd note (differences that I also commonly hear cited):
1. Independence. The ability to set own bylaws. The ability to speak out on issues as your group sees fit (local PTAs are prohibited from or strongly encouraged not to speak out publicly against PTA positions). The ability to operate in the fashion you feel best fits your school. Don't have to charge dues if you don't want to (dues required if you're a PTA).
2. Welcoming/Collegiality. Whether you agree with PTA's political positions or not, the fact is that taking political positions often works against goal of bringing all parents together. So here, it largely depends on your goals. If your goals are to build involvement, create community and support the school -- then PTA politics can get in the way of that. (Will parents who support vouchers feel attracted to your PTA?). But if your goals are to be active politically (even if that means turning off some folks who don't agree with the politics), then PTA can work well.
Sounds like you're hoping your group can look into difficult questions, discuss, debate and work on solutions. That could be great. You could do that as a PTO (PTOs can take any shape you like) or a PTA.
Sounds to me, though, that perhaps your group would be outside of PTO or PTA. Perhaps let a more standard PTO or PTA flourish and create a separate group for what you're after. We see more towns, for example, creating LEFS (local education foundations), which often take on this type of role for their district. Could be a thought...
Good luck,
Tim