Since this was my idea, I reckon I'd better explain why I think it should be a category.
First, however, I would like the clarify that I think the award should be for the comic that has improved the most during 2009 - before that doesn't count, giving shorter comics a better chance, and reducing the workload of the judges.
My main reason in support of this award is that I believe improvement should be recognised. A lot of webcartoonists put a lot of effort into their comics, and many of them actively try to improve both their writing and their art in the course of creating a webcomic; some people create a webcomic for the purpose of improving. This kind of effort and hard work should be recognised.
This kind of award is also quite inclusive. It can include both relatively new comics and older comics. Generally, though, the big dogs won't fall under this category, so it gives lesser-known comics a better chance.
Some people have argued that this can be seen as a backhanded compliment - "yes, you're good now but you used to suck". I disagree. This isn't the "worst comic a year ago" award. While it's true that some of the nominated comics will have begun, shall we say, below average, that will not necessarily be the case. A comic that's been going for five years, and has always been average to good, may still improve - perhaps the artist went on a life drawing course, or the comicker decided to reduced the frequency of updates in order to spend more time on each page, or in some other way made their comic better than it had been for the last four years in a significant way. So while it might be that one nominee began pretty bad and became average to good, another might have began fairly good and became wonderful.
So in summary, the "most improved" award recognises hard work where it might otherwise be overlooked; it includes a wide variety of comics; and while it might be seen by some as a backhanded compliment, it is not intended to be.