Being from, and currently residing in Lincoln, I figure I'd chip in my two cents.
Fish store is ok. It really depends who's working at the time. Some of their staff knows a good deal, others, not so much. I went in asking if they had a glass CO2 diffuser, not thinking they did but it was worth a shot, and was met with blank stares. I had to actually describe it. He offered me a pack of bubble stones... They have decent plants, some unusual fish. They have a brackish tank that's neat. Their salt water selection is the best in town. One thing I will never forget about this place is once I went in and noticed their glow light and black neon tetras were covered in what can only be described as an major outbreak of ich. When I informed the staff, they seemed not to care.
Fish World is my favorite.. however, recently their selection has gone down hill. The owner is very knowledgeable about fish. Once I noticed they had a green mandarin dragonet. Really pretty. I asked about it for my salt water tank. First question was "What does it eat" His response "Not much of anything. That's the problem. Research the fish and come back. If you still want it, I'll sell it to you" I did just that and found out what it ate and realized I would need a couple of months at least to establish a food source for it. Not many salesmen will talk you out of a sale. Like the Fish Store, when I went in one time and noticed one of the tanks had ich, they started treating them right away and flipped the price signs on that tank to indicate they weren't for sale. As stated, the owner knows nothing of plants and has admitted to me he simply can't keep them alive. Their plant selection is terrible and over priced... however, the 11 dollar anubias I got from them three years ago is still going strong and now dominates almost half of the 55 gallon aquarium I put it in.
PetCo on O street... fish supplies is the only thing I buy there. Their fish always look bad. And typical of most big chains, they often sell terrestrial plants as aquarium plants.
PetCo on S 56th has MUCH better fish. The manager of the fish section knows a good deal and often gets in some more exotic fish. Their plant selection is better than the other PetCo. Looked all over town for a run of the mill amazon sword... this was the only place that had one that wasn't dead or dying.
PetSmart on N 27th.... Fish supplies only for me. Their fish always look sick and their tanks are often littered with dead fish. Their plant selection is ok, however most of them will need serious work to just keep them from dying. They do however carry more plant care products than PetCo. Fish Store still has them beat though.
PetSmart on Pine Lake Road is better. Their tanks generally look better, though the selection is small. Beware what you buy though... When looking at their Pacus (which I strongly disapprove any big chain from selling), I noticed one that looked just a little different... and had very sharp pointy teeth... not to mention several of them had noticeably chewed fins. Selection on supplies is about on par with other big chains.
Side note, parking at The Fish Store is awful. I think there's a total of 7 parking spaces. Parking at Fish World is great... just wish they had a better selection.