Bought my 2010 C14 new last fall in Sept and just rode it stock thru the fall. The power is great, but I would like to help with the drivability of the bike. You can definitely tell that the mapping is way off and the effect the flies have on the engine.

Now I know there are two solutions considered to be most desirable to fix it. First would be a PowerCommander with the flies removed, the other is the Gull Re-Flash with the flies removed. I believe I understand the pros and cons of both:

PC:
Pros
 Its adjustable for future upgrades (ie exhaust, intake, etc...)
User Adjustable

Cons
Its adjustable (LOL)
Its only as good as the tuner.

Ive had PC's before, and they seem reliable, but I had issues with both of mine on my H-D's with water getting into them, and periodic need to re-flash the map.

The Gull:
Pros
Refined, many different configurations all tuned by the same guy on the same dyno.

Cons
Locked into the configuration you currently have, or may have (I would have them map for the CS-One I would plan on getting down the road).

Are there other options out there I am not thinking about?

Dynotronics also does the ECU flash.  With the C14 the PCV is protected from the elements unless your bike takes a swim.  I have had zero problems with mine over the past year and half, or so.

If you have a reflash done you don't have to remove the flys. They can be programmed to open sooner.

If you have a reflash done you don't have to remove the flys. They can be programmed to open sooner.

+1 

Now I know there are two solutions....

That's debatable if you consider the Auto tune as a third option with the qualifier you used as "most desirable".
There is also the work involved and the effect of each option on the Traction control and any warranty issues to consider.
 I asked a similar question almost a year ago, although I possessed less understanding at the time than you do now. I received some great information to my questions in that thread.

I still haven't done anything (other than to make a decision) in this area yet, but my decision is to get the Guhl reflash.  Of those that make changes on the 2010+ models in this area of the bike it seems that most are doing the reflash, but my perception may be biased as I unconsciously seek
external reinforcement of my decision.    I've yet to hear of anybody complaining about their Guhl reflash, no one to my knowledge
has posted "fricken reflash! I wish I had just pulled my flies!" If there are any maybe this thread will draw them out to share with us?