That all being said, here's my "solution..."
First up, make some loot balancing decisions. Make opening that chest behind that dragon worth my time and effort spent kicking his ass. Yes, I want some treasure, this is a fantasy RPG, dammit! How many RPG's have you played where almost every single kill got you some gold?? More than some would be willing to admit, I'll bet. If you think the game is going to have too much money, then just raise the prices on the really nice loot! So what if Farwick is selling a Longsword +8 of Flaming Wrath for 100,000 gold?? It'll make it that much sweeter to see the look on his face when you toss that amount onto his counter (he'll probably be really pissed when the weight of 100k gold pieces destroys the counter... ^_^). I've personally be disappointed more than once when I found a chest in the middle of nowhere like it was supposed to be hidden and it had all of some weapon fragments and a smelly looking bandage. That's the sort of stuff that encourages the "re-rolling" of the loot.
Second, for those that still bitch and moan - which I'm almost positive is a very small percentage - introduce some options that will satiate them... at least until they find something else to bitch and moan about.
Now I know you're planning on maybe introducing some checkbox options, but I don't think that really is the best answer. I propose instead introducing a few playing-style options. Similar to difficulty levels, but not necessarily being more difficult. Here's my example..."Classic Mode"
Same style as Book I. No save/load limiting, the treasure is randomized when you open the container. Assuming the loot system is balanced, I don't see much re-rolling anyways. No headaches here. My guess is that the vast majority will choose this option... at least the first time around....
"Challenge Mode" - Scoring begins here.
1 Minute Save/Load Limit, treasure (and shop loot) is randomized when you enter an area. No save during combat. Loot quality increased 10%. Each shop has a special high quality item for sale (at an exorbitant price, of course).
"Extreme! Mode" (yes, with an exclamation point, it wouldn't be Extreme! otherwise
)Save/Load limited to leaving an area, treasure (and shop loot) is randomized at the beginning of the game. Shops only restock monthly. Loot quality increased 15%, Scoring 10%, Experience 5%. Special high quality shop items are "leveled up."
"So You Think You Know Eschalon? Mode" Save/Load in Towns only, treasure randomized based on a seed created @ installation. Shops only restock monthly, and shop owners offer 20% less for your loot. Enemies do 15% more damage. Loot quality remains @ 15% increase, Scoring 15%, Experience 10%. Shops' high quality items are retained at the Extreme! level. The Four Dragons of Fate have appeared in the game world, and each guards an "ultimate" weapon. Getting the "Destroyer" title was baby stuff compared to defeating one of these puppies...
Now I'm no programmer, but I'd guess having set "difficulty levels" would be better than having a bunch of checkboxes, and would be less stuff to have to test during beta. I know I'd rather not have to worry about testing each individual checkbox feature to make sure it works (speaking from experience in QA'ing software ^_^). I'm sure there'd be a bit of tweaking of the percentages and such, but that's all part of the process...
So there you have my "take" on the "issue." Call me crazy (I certainly already have...), but I think there's enough there to make everyone happy, even the occasional elitist snob. Now then, if you don't mind, I'm going to jump back on my rogue... I've got some sneaking around to do.
