I generally stay away from the ‘scale’ and ‘replace’ modes, due to exactly this. This is actually more of a maya usage question and not related to the tools.
First, I’ll cover my skin settings:
Skinning Method: Classic Linear
Normalize Weights: Interactive
The normalize weights setting is the really important one. I believe by default this is set to ‘post’ which is terrible.
As for how I skin, I basically use nothing but add. If I want to remove weight from one influence, it really just means I need to add that weight to another influence. Doing this leaves nothing to chance. The problem with replace, smooth, and scale, is that you’re leaving it up to Maya as to what to do with the weights, which is never good.
Also, when I skin a character, the first thing I do is flood the entire geometry to the pelvis bone. I don’t keep any of the default weights maya provides, as I find it takes more time trying to clean it up and fix them, than it would to just do them myself.
I will use smooth now and again, but only under super tight restrictions. First, I’ll lock down all influences except the two or three in the area I’m trying to smooth. This prevents maya from throwing weights were I don’t want them.