Getting a wavier is not a good thing. It means that something in your history is a possible disqualifying factor. These can be something in your medical history, which is the most common, or law violations and even some waivers for ASVAB score. However, if you're in the process of getting a waiver it's also a good thing because at least you haven't been DQ'd on the spot and the higher ups are giving your case a chance.
The most common waivers are also the toughest to get. What's different about medical waivers as opposed to moral or score waivers are that you can't change your medical history or get rid of a medical issue (for the most part). Moral waivers, for things such as speeding tickets or jail time, are easier to show improvement. If you went through a string of traffic tickets and have gone without one for 10 years, they can see improvement. If you scored low on the ASVAB, but show a lot of potential they can see that and hope you improve. However, if you have diabetes you can't just "teach" yourself not to have diabetes anymore (although diabetes was a bad example, as that is one condition that is automatically disqualifying, but I hope you understand the idea).
During your initial physical at MEPS you will meet with the head doctor before you leave, s/he will look over your medical packet and will determine if anything in there is automatically disqualifying, if you need a wavier, or if you're good to go. Then you give that doctor's recommendation to your armed service office at MEPS and they will take it from there and the higher ups will decide your fate.
BUT, there is more! What if your case can't be decided at your local MEPS? Well, they send you off to Washington D.C! Just kidding, not you, but they do send your packet to Washington for the head office of your branch to decide.
For me, my medical waiver was sent to the Air Force Surgeon General's office for consideration. If you have a moral waiver that can't be decided at MEPS your waiver will be sent to the Judge Advocate General's office for consideration. This works the same as MEPS they will either qualify you or disqualify you.
Links
The PDF that I'm going to link to you is not one to base your enlistment case upon. This PDF is used by the Air Force to determine if one qualifies for a FLIGHT PHYSICAL and NOT ENLISTMENT. However, it could be something that might give you insight into how severe your condition may be.
(It's also, very, very long - use the search feature! or look for your condition in the table of contents and jump to that page)
Waiver Guide