Take two standard NPC fighters from the DMG.
#1 - Normal lvl 6
Str 16, Dex 13, Con 14, Int 10, Wis 12, Cha 8
HP: 49, Atk: +10/+5 mw greatsword (2d6+4)
#2 - Fast Healer lvl 4
Str 16, Dex 13, Con 8, Int 10, Wis 12, Cha 8
HP: 22, Atk: +8 mw greatsword (2d6+4)
With the -6 Con you'd give alongside fast healing 3, you've basically doomed #2. He's two levels lower and has less than half the number of hit points. He has two less feats, two less HD (thus affected by sleep and other spells which are based on HD), and his saves are noticeably lower, particularly in Fort which is 4 lower than the normal fighter.
Sure, if he survives (not likely at that level), he'll heal up really fast. Pit them against each other and #2 will be down on the average of three hits, while #1 will be hit less, and be able to take twice as much damage.
Not a good trade off.
Let's try LA +1 instead.
#1 - Normal lvl 6
Str 16, Dex 13, Con 14, Int 10, Wis 12, Cha 8
HP: 49, Atk: +10/+5 mw greatsword (2d6+4)
#2 - Fast Healer lvl 5
Str 16, Dex 13, Con 8, Int 10, Wis 12, Cha 8
HP: 27, Atk: +9 mw greatsword (2d6+4)
Prospects still don't look very good with that Con penalty, he's just over half as many hit points.
Let's ditch the Con penalty and try again, with a LA +2.
#1 - Normal lvl 6
Str 16, Dex 13, Con 14, Int 10, Wis 12, Cha 8
HP: 49, Atk: +10/+5 mw greatsword (2d6+4)
#2 - Fast Healer lvl 4
Str 16, Dex 13, Con 14, Int 10, Wis 12, Cha 8
HP: 34, Atk: +8 mw greatsword (2d6+4)
So, that's two levels behind in saves, bab, feats, etc. He has 15 less hit points, but fast healing 3, which amounts to basically 5 rounds of healing, although he'll be lucky to last 4 rounds against #1 in average numbers. This seems just around the balancing point for fast healing 3, although I'd say still a touch weak.
General conclusion, fast healing 3 seems just about balanced at LA +2 without any penalties, and might merit a small bonus. Anything below fast healing 3 should probably drop to a +1 LA if no other benefits are given.
The other place to do an analysis would be with the fast healer level 1, and the normal level 3. But I imagine a similar trend would be apparent as the above.