Fit is highly important. Fortunately, I stumbled into a properly fitting bike when I got back into it about 18 months ago. I walked into Wally World, did a stand-over check, and said, "I'll take this one." But in hindsight, I don't recommend anyone do it like I did.
One of the chief benefits of going with a mainline bike from an LBS is long-term repairability. Everything on nearly any bike will work great at first. But on a mainline LBS type bike, you will be able to find parts and get repairs done nearly anyplace. But that may not be the case with a department store bike. Also, if you can work a deal with your LBS, you will be a jump ahead in terms of what is known as "good will." Like any business, they tend to remember their "got it here" customers with a subtle degree of gratitude that shows up on various ways.
My next suggestion is to see if you can locate a recent copy of the Bicycling Magazine 05 buyer's guide. Several hundred different bikes of all types are reviewed there, and you can glean a lot about what might suit your needs & interests, and what are the merits of different frames, handlebars, crankset, cassettes, brake configurations, etc., just from reading that particular issue.
Also, locate the thread on the commuter section of this site with pictures of the various member's rides. You might get some good ideas there.
Getting back into cycling, I decided to go as cheap as possible "in case I didn't like it." As a result, I did not really drop a lot of coin in the purchase, and the low budget bike has not hurt me because it works fine and fits right. But, I'm all but addicted to a daily, rolling "fix" on two wheels, and am constantly meditating on what my next bike will be. And there are several in the buyer's guide that will allow me to do my exercise riding, make an occasional jaunt with some locals, or even hang bags on it for a weekend tour. I've read my copy at least three times now, and am down to making notes on specific models.
Today, I am lusting after a Specialized Sirrus ...
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Current bikes: Unknown year Specialized (rigid F & R) Hardrock, '80's era Cannondale police bike; '03 Schwinn mongrel MTB; '03 Specialized Hard Rock (the wife's)
Gone away: '97 Diamondback Topanga SE, '97 Giant ATX 840 project bike; '01 Giant TCR1 SL; and a truckload of miscellaneous bikes used up by the kids and grand-kids
Status quo is the mental bastion of the intellectually lethargic...