I'm going to answer the OP as neutrally as I can (I haven't read anyone elses comments, so forgive any repetition).
In terms of wide open flexibility, you might want to look into Pathfinder. You sound like you have done your research and are already leaning towards a more 3.x based system, and I can say that its definitely a lot of fun as long as you keep on the ball, which again, you sound like you are willing to do.
I haven't actually playtested Pathfinder myself, I have read through it however, and from what I understand its pretty backwards compatible with most of the 3.x system.
The only warnings I might give are that you could get caught up on the CR system of encounter building. It takes a little work, and you will definitely need to know what your player's characters are capable of and where their general power level sits at. The CR system is more a rough guideline than a definite 'budget' for encounter building, and things such as resistances, gear, and min/max point spreads might creep up. However, with a little practice and a few trial runs you should be fine and generally know where the characters are most comfortable.
I'd recommend stealing some things from 4e as well, however (That is, if you don't decide to go with 4th edition that is).
Minions! You can definitely use minions in 3e with a little tweaking. I'd recommend it if you plan on sending hordes of undead at the group. What better to strike fear into your PC's than to send 20 shambling undead screaming towards them.
I'd also recommend looking into skill challenges of some sort. They're wonky to read about in 4e, I'll grant you, but there are several threads and a ton of podcasts/editorials about the subject. Its not something that a game needs, but if you are looking for more rules-driven out of combat things to do, skill challenges are right up that alley.
Lastly, I'd recommend playing a one or two shot game of both systems. You can get Pathfinder for free (Its the beta I believe, but it's a full book download that includes some *really* good artwork). You can also download the Keep on the Shadowfell adventure, the quick start rules, as well as the demo of the 4e character builder that lets you make PC's of up to 3rd level (Which is perfect for the Shadowfell module).
Its definitely a touchy subject to some, but there's lots of choice out there. Don't let anyone get you down about what you ultimately choose to play. If you and your group is having fun, nobody can argue that you are 'doing it wrong'.