I don't really have much trouble with barre chords when strumming, but when it comes to fingerpicking with barre chords it automatically turns into hell!

How do I keep the D and G string from not getting muted? -__-
keep practicing is the only advice that actually works
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If you aren't having trouble with barre chords while strumming but you are with picking then your strummed barre chords probably need help too. Barre the fret with your first finger then practice that until every string rings out, then drop one finger at a time etc.. They aren't going to come naturally within a week or month even. Takes a while to develop a solid barring technique. One day they will come so natural that it will feel like you are playing an open E. Hope this helps!
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Oddly, I find that when a string fails to sound in a barre chord, it's usually a note in the barre that's missing, not the fingered notes. ( E-1, B-2, or E-6 in the "E" open formation).

How about arpeggios with a pick, are you still missing notes?
Man I wish I could play a solid barre chord....
I had this problem and I realised that it was cause my posture changed slight when I switched to fingerstyle. I just kept pracrtiscing and I fixed it
You need to do some finger stretching exercises on guitar each day for around 10min, that will help you enormously after about a month. There are some very well known ones that work well.