Big pond, here's a little more of my thoughts: TS are just about essential for maximizing a BOW's potential for big bass - they make a huge difference in the average size of the bass, as well as the maximum size of the biggest bass. If huge bass are your main interest, don't hesitate to stock them as they'll make a big difference. But if catching big bluegill is also important to you, don't stock shad or a couple years from now you'll be back on here trying to find a way to salvage your bluegill population from stunted growth.
I personally feel that the studies that try to claim that TS or gizzard shad either one do not affect bluegill size, are at the very best poorly substantiated and researched with shoddy methods and conclusions, and at worst just skewed science.
Trophy bluegill are my main species of interest. I still fish regularly for bass, but I fish a great deal for bluegill, and I've fished a lot of BOW in several states, both public and private, in the quest for trophy 'gills. And I've never once seen a pond or lake into which TS or GS or golden shiners were introduced, either intentionally or otherwise, in which the average size structure of the bluegill was not cut at least in half. Not once. I'm managing a 60-acre lake right now that, according to the owner, once had "huge" bluegills; the first time I spoke with the owner, he commented that he didn't know what had happened to the bluegill because they were a fraction of the size they had once been. Turns out that five years ago another pond manager stocked TS and GS in the lake. The bass are far bigger now than what they were pre-shad; the bluegill average about 4".
One study that claims, without solid science, that shad have no adverse affect on bluegill, notes that the size structure of plankton is invariably altered in lakes that are stocked with shad: the plankton increase in number but become smaller. Any biologist on here will readily tell you that to maximize your bass growth you have to have large prey for them to eat - so why has no one made the obvious connection that if a bluegill population's food source suddenly goes down significantly in average size it can be expected that the bluegill will suffer a corresponding decrease in growth? Also, bluegill very much use open water, especially the larger ones; anyone who tells you they don't is not a bluegill fisherman. I've caught hundreds if not thousands of large bluegill in the center of ponds from four acres to over eighty, in open water with no cover anywhere near.
Even if shad didn't directly compete with bluegill for plankton and also lessen the quality of that particular food source, just the effect that they have on bass predation on bluegill is enough to cut the bluegill's average size drastically. Shad are fusiform prey, which means they're more ideally shaped and therefore easier for bass to eat at larger sizes than bluegill; they also have weaker dorsal fins that are far less threatening to a bass than a bluegill's; when shad are introduced, bluegill go from being the primary prey, to being an afterthought when the bass can't catch a shad. The bluegill overpopulate, at which point their growth stops altogether due to too many numbers for their food source.
Hopefully this doesn't come too close to a rant, but it rankles me that there is literature out there that claims shad don't impact bluegill growth. I think your solution is still CJ's suggestion: make the larger pond your trophy bass pond, and the smaller one your trophy bluegill pond. A ten-acre lake can support several real trophy bass in your region, and several more in the three- to six-pound range; you can load it up with bluegill, TS, GSH, GS after a couple years, crayfish, and tilapia and fertilize it monthly so all the bass have to do is open their mouths and inhale; and you can plant a couple automatic feeders on the smaller pond, put three or four tiger muskie in there to put the fear of God in those bluegill and adjust their density, and set the feeders to three times a day, and within three or four years you'll have bass approaching ten pounds (assuming you stock tiger or Floridas) in the big pond and bluegill approaching two pounds in the smaller pond. You'll have the best of both worlds, and will never have to learn firsthand how TS are bluegill kryptonite.
