With regard to tone controls, I find that there are a few areas with solutions, and some others that demand new software. For LPs, there are a few vintage pre-amps that offer different EQs, other than RIAA. The Mac C-8 actually allows the user to set the eq with 10 switches. This was developed to accomodate the many early EQ formats.
In the case of a basically Good system with some minor Room issues that tone controls might fix, I would suggest looking into the room issues more closely. I realize that tone controls have a higher WAF/SOAF but if the room problem can be IDed and fixed, one might get a significant order of magnitude of improvement - these could be little things like moving the speaker in/out a few inches, etc.
Sean has a good suggestion vis external boxes connected through loops. There have been a few preamps that offer quality tone controls, Cello, Metaxs?, etc, but they are expensive.
Yes this area is over looked, but it is a trouble some area to solve well.
Good luck.