It's a question of application. A flat bar is better for some things and a drop bar is better for others.
On road it's all about pedalling efficiency, what a drop bar gives you is a better position for cycling and at least four different hand positions, handy in long rides as you can offset upper body fatigue by switching positions.
Off road it's all about control, a flat bar lets you exert a lot more control on the bike to get over obstacles etc. I don't have much use for that commuting, even on shared paths.
If you do decide on drop bars, it's important to get them set up correctly. I'm a commuter, not a racer, so the flat back ideal of a racer is not what I'm interested in. My riding position's almost as upright as my MTB position. A good explanation of handlebar position can be read here
The Trek 1200 is a good bike but there are caveats. The wheels that came with mine were pretty rubbish, maybe that's changed but I'd have a good hard look at the wheels. You'll save yourself dollars and pain if you get them upgraded to something decent when you buy the bike.
The running gear's 53/39 on the front which is a traditional road set-up. I found that OK for the first eighteen months but ended up upgrading to a compact 50/34. I find that a much more useful set up for my needs.
Trek isn't the only kid on the block. Much as I love my bike if I was shopping for a commuter today I'd be looking at the Cannondale T2000, Jake the Snake, Surly Cross Check or the Surly LHT. If I'd done that four years ago I'd have a nice road bike as well right now
All that said the Trek 1200 has been very capable, very reliable and you'll part it from my cold dead hands.
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