Unless you have a really nice set of markers or you're working on a large painting, color digitally. There aren't a lot of physical media that allow you to create quality colors that scan well. In other words, don't blame the scanner if you're scanning colored pencils and expecting it to look like something a pro did with copic markers. A quality scan from a $2000 scanner will still look about the same as that from a decent $30 scanner. (Also, a good set of markers can easily cost several hundred bucks...)
If you decide to scan lineart, avoid pencil lineart. You'll almost always want to ink, either using nib pens or pigment liners. If you want to do a more cartoonish or American style, you can also use a brush. Erase your pencil art and scan grayscale (300 dpi), then do a levels adjustment so your whites are white, your blacks are black, and the contrast is strong.
Finally, drawing with just a tablet and Photoshop isn't hard, even when you have a tiny Graphire. You have to approach it differently though. Instead of doing lots of sketches, a final draft, and inking, you explore the possibilities -- making as many small or radical changes as much as you want, until it's perfect.
For example, you can start drawing a person by creating a throw-away layer that you use to experiment with different postures, lower the opacity, then create a new layer on top of it and draw the form on top of the figure. (Note -- This helps prevent the stiff, unnatural figures you end up with when you focus on drawing the details, say from top to bottom. If you aren't doing this, then start.)
Zoom in and out, or flip the image horizontally if you need some perspective. Taking breaks is another good, but more time-consuming alternative.
When you have a dynamic figure that expresses the feeling or idea that you had in mind, then you can draw your final version on top of that.
And be sure to experiment with different brush settings and sizes. Depending on your drawing style and process, you might consider giving Corel Painter or OpenCanvas a try.
