1. You've pretty much nailed the primary difference between the Sedona and Cypress on the wheels.
2. Suspension forks at price point you're shopping is false economics. They invariably lack lock out, are heavier, will rob you of top end speed, has to be maintained, and is one more moving part that could potentially fail. Wider tires, decent grips (Ergon's rock), and gloves with gel inserts will give you plenty of comfort.
3. Since this is your first bike purchase, I'd advise you to stay away from bikesdirect and other online sources. Any adjustments or tweaking would have to be done by you (and you might have to invest in some specific tool(s) to do so), take it to the LBS anyway, or worse yet, ship it back- after waiting for a RMA confirmation.
4. Buying from the LBS allows you to test ride before you buy, the initial set-up/fine tuning to ensure fit is generally free, and most shops include some sort of service after the sale for free as well. What type and for how long will vary.
5. Don't get caught up in the frame material war at this point nor the component one either. You'll likely not notice the characteristics of frame material within your budget (except maybe for weight) or the performance of the components like Alivio, Altus, Deore. FIT is the key- you will notice if you're too cramped or too stretched out.
6. If you're now considering the lower end of the Trek FX line (and that brand is overpriced IMO), then that opens things up a bit into the 'urban' and 'fitness' spectrum of the hybrid universe. I could throw make/models out, but I don't know what is available to you locally.
7. Don't know if you have a REI near you, but strongly consider buying from them. From all accounts, their return policy is outstanding. If you get something and find you don't like it, they'll take it back. And if you get their Novara house brand, then you are golden as far as warranty goes. There was a poster up in commuting who had a Novara bike that he bought more than 2 years ago (think it was closer to 5 or 6), trashed the frame in a collision, didn't have a receipt, REI couldn't find a record of the sale in their system... and they still gave him credit towards a new bike!