There's a current thread on filtering a store. There's also a thread discussing the profit levels of a LFS. Do a search here on MFK.
I'm not a proponent of central systems despite understanding the rationale.
IMO, if you try to make YOUR STORE look like someone else's store you're creating an image problem. On the other hand, if you can incorporate good things from someone else's design into YOUR design without having customers realizing someone else uses a similar set-up, go for it. Use different colors, different shaped tanks or something.
I don't understand the rationale for high pH and low pH set-ups. Unless your customers duplicate that particular set-up they're going to put those fish into conditioned tap water. I'd recommend setting up a single tank optimizing conditions for some of those fish and offering handouts to duplicate those conditions.
I've done several stores and concluded that isolating areas doesn't create the best traffic flow. I originally thought keeping SW and FW in separate areas a good idea. (Obviously, your customers need to know whether the fish are FW or SW. You'll have to address that issue somehow.) Eventually I removed a wall to create better light in the SW section, increasing the visibility of the section increased it's traffic. I had previously kept the supplies separated also. After combining FW and SW products, thefts went down and more customers were handling things they wouldn't have picked up before. Relating to thefts: pocket-able items or expensive things need to be behind the counter, a glass door or at the very least adjacent to the counter.
I'd think proper placement of the counter is very important. Being too close to the front sometimes inhibits entry to customers. I'd consider somewhere in the middle, centralized in the store. Reasons? Visibility and access. If you're at the front all the time walking to the back takes time. If you're in the center, going to the front or rear of the store is easier. From the center it's easier to monitor the whole store.
Another thing, I've always wanted to add, but never have, an enclosed area for display. A boxed-in cube, like the puppy adoption area at Petland, but using a top-of-the-line tank set-up in a room-like venue. Maybe using a loveseat, tables and lamps opposite an entertainment unit featuring a nice tank. It's possible that a furniture retailer would provide the furniture for advertising either at no charge or drastically reduced expense.
In choosing the tank size of store tanks you need to consider how you're going to purchase your stock. If you plan to buy from an importer or farm you're probably going to buy in box or 1/2 box lots. A 20H isn't as functional as a 29g, not enough surface area. I also agree that you'll probaly want some larger tanks for big fish. You'll probably wish at some point that you had some smaller tanks too. A bank of 10g is beneficial for oddball fish or the remnants from previous purchases. Of course, if you plan to buy locally, you won't require the bigger tanks. You'll just have to pay an extra person (the wholesaler) for the stock you choose to carry.
I hope this helps. Dan