Make use of possibility to have various layers in gimp. Also, pixel editing can be performed in gimp as well, setting airbrush to hardness 100, size 1 and flow close to 100 will do.
For color intensity, well some in-game icons feature less contrast, those are usually the drawn ones. You can edit colors by gimp tool hue saturation and reduce or increase highlight tones by curves.
There's a lot of things in Gimp that are annoying for pixeling.. There's not much I can tell right away but for example the selection tool is different than in paint, in paint I'm a lot more accurate when selecting pixels than in Gimp, which in some situations can be quite a nusiance.
I don't play much with the features in Gimp but I do hue edits (been doing that mostly just on the blue borders I add), brightness edits to make the darker inner edges of an icon and I increased sharpness on my Shadowhunter Lujka icon. Haven't tried the curve tools for highlights, I'll have to look into that.
I was trying out Krita before (posted some Krita sketches on here in past), it's very similar to Paint in terms of hotkeys and appeal, so it's easier to make the Paint to Krita switch than Paint to Gimp, but I generally just stick with Paint.. Especially on these kind of icon edits where I don't see a need for layers.