I was a manager at a Borders for many years. The store that I was at carried 175,000 book titles, not copies, titles, I think it was 210,000 titles altogether, with DVDs, CDs, etc. I do not believe there is an independent bookstore anywhere that could possible come close to this total. Many times I have tried to purchase books at indies, such as the latest Vonnegut book, only to be told that they did not stock it. The breadth of selection at the chains is huge. They carry the small press, the literary fiction, practically everything published (7,000 titles/year last time I checked). Selection is what they do and why they are able to exist. If they didn’t have that and only sold the bestsellers at their discounts they couldn’t last, see Crown/Super Crown.
However, the indies have an advantage in that they can specialize. Some of the best performing indies are the ones going after the niche market, the mystery stores, the sci-fi stores, the Christian stores, and so on. By having the smaller choice, they can become more intimately aquainted with it and thus are better able to make recommendations. Also, they are better able to know their customers. They can remember Mrs. Jones, and that she bought such and such title last time she was in, and can suggest a title to follow that one.
The staff at the chains can be very hit or miss. There is always a core of people that have been there for years, these are the book people. They know the inventory and make recommendations just as well as any indie seller anywhere. The much larger percentage of staff are merely people holding down a job. They, perhaps, would be just as happy at the Gap or Pottery Barn. If asked for a recommendation, these are the ones that can’t get past the bestsellers. Since they are the majority, these are the ones that most customers see, thus the bad reputation. If you, the customer, want a good book shopping experience, you must find one of the book people.
Both chains and indies have access to the same ordering processes and can therefore order anything in print and many titles that have gone out of print, just like Amazon.
We have several excellent representatives from both camps here in Chicago. We also have poor examples in both camps.
So I suppose, in reference to the OP, shop at whatever store you like best.