A few personal observations (I've never been to Tropical Isle- so no comment).
1) Underwater World has a great selection, and while they aren't the most outwardly friendly crew (who can blame them, they're in a mall and the vast a majority of foot traffic is "just looking" or kids pounding on glass), they're good and helpful. Underwater World is the place to go for rare/unusual fish. They've had some Rays on display for months, and a number of sharks, as well a some hard to find angels and other unique fish. My only gripe is that because of the amount of livestock they keep, I've spotted a lot of unhealthy looking fish (thin mandarins, lots of ich, etc.). QTs are important regardless, I still buy fish from UW, but be vigilant. Their live rock selection leaves a lot to be desired. The coral selection is good, but other places are better (and healthier, IMHO).
2) The Coral Reef is outstanding for both coral and fish. It's also one of the few places that is exceedingly honest and won't sell you something you shouldn't have in your tank. They say it themselves, but they're hobbyists first. Someone else already mentioned it, but a lot of the livestock on display isn't for sale. It's a great store and you can expect healthy livestock and expert advice. It's not the type of place you're going to find exceedingly rare, controversial, or hard to keep fish.
3) Love the Reef is the best (by far) when it comes to coral. It's pristine, and Yorgos and his team knows their stuff. There's an excellent variety, good equipment (not much of a markup). Again, I have yet to see a place that has a better variety of coral, or healthier coral. They have everything from $10 frags to healthy, pricey colonies. I've had fewer pests on my coral from LTR than from anywhere else. They've also adjusted to my system faster than coral from anywhere else. The selection of fish is OK (though they had a lot of great designer clowns when I've been) and what they do have is healthy.
I also feel like I've got to mention Animal Instincts in Fall River. They're not huge (lots of FW and reptiles), but they have a decent selection of healthy fish and some of the best premium Live Rock I've purchased anywhere in the area (all sorts of good hitchkers- even small Zoa polyps and a mushroom). They're also good with special orders. The staff in the aquatic area are all hobbyists and know what they're doing (one of the guys recently had the contents of his home tank on display in the store because he had a crack/leak at home). It's not a huge operation, I don't know that it's worth a long drive by itself, but it's worth a stop if you've made the drive to see Underwater World and the Coral Reef since it's in the area.
Speaking of rare/unique fish, I stopped into the Petco in Woburn (Commerce Way) on Friday. They had a ton of fairly unique fish- some I've never seen in a store before. Unfortunately, many looked unhealthy (some very dead fish on the bottom of some of the tanks), and the tanks were wildly overstocked. I guess Petco either owns or has a partnership w/ LiveAquaria so I think a lot of the petco stores will start carrying a wider variety of fish. It's sad because they don't have the knowledgeable staff to care for them. This is the worst I've seen it yet.
