Generally mud in mixes isn't a problem with a specific instrument or sound, its a general problem of too many instruments with content in that mid range. For instance you could create a mix where the only instrument playing in lets say 200 - 400hz is a synthline, but in reality guitars, drums, bass, etc all have different components of their sound which can extend into this range. One solution is to totally cut this content from these sources, but this will have a nasty side effect of killing some of their harmonic content and making them sound weird. It also likely leads to thin mixes like you were describing, your earlier problem of cutting away too hard in that region.
My approach with this is to listen to my mix and decide on which instrument I want to have occupy this mid range region (normally with some form of eq visualiser). I will then apply complimentary eq, I will slightly dip the other instruments in that region, unless I am sure they should have no content there - in which case I use a filter or a notch to cut that area out of them. This approach stops them from sounding strange, and still gives a strong mid range to the mix as a whole (Try to avoid cutting more than about 3db over an octave range, this way you shouldnt leave anything too thin).
As a final note, when you cut 200-300hz across the entire mix, you are actually cutting that range in every instrument, its like applying a cut on them all seperately. This really doesnt solve your problem of having clashing instruments in that range. You will have the same mud, just quieter. An effecient option could be to bus all the other instruments except your chosen one, for that range, together and cut the mid range on those all at once. That would still leave the one instrument in the mid range.