Knowledgeable staff is the primary thing missing from most of the LFS in my area. I routinely hear the employees giving out some really poor advice/misinformation to customers. There are a few more knowledgeable people scattered around between the LFS', but they really are diamonds in the rough.
I get a lot of blank stares when I go into one looking for what, in my mind, is or should be standard aquarium equipment.
Naturally, healthy fish aren't always available, and the plants in every one of my local stores look like garbage. (There are a few further away I haven't been to, just to be fair.)
One other thing that most LFS don't have (with the exception of one store with excellent stock that's located 45 minutes away) is minor hardware, and general aquatic equipment. I'm referring to PVC hoses of different size, bulkhead fittings, universal strainers, glass/tile hole saws, replacement impellers, and things of this nature. I also can't find those universal, circular sponges for placing over filter intakes anymore.
For these reasons, I buy >90% of all my aquatic equipment, and livestock online. It's not that I don't want to support my LFS', and price is not the issue. They simply don't have the things I want or need, and generally don't have the knowledge or experience to be of much help to me.
The only thing I really buy in the LFS is frozen food, light bulbs (sometimes), and the actual tanks. If there was a well run, well and healthily stocked, LFS in my area with knowledgeable staff and basic hardware, I would gladly shift all of my purchasing to that location, even if prices were 30%+ higher than online (which they generally are).
There are 4 pet stores within ten minutes of my apartment, but the only one I generally go to is 45 minutes away.
I also prefer LFS that have self contained tanks, rather than one system all the tanks are hooked to. The majority of LFS in my area don't quarantine new arrivals either, likely because that would take up alot of space.