A couple of years ago, I bought a beautiful used Martin guitar 000-28VS (12-fretter). It had some neck issues, so it was quite cheap for this type. This is fixed now, but the more I play it, the less I like the sound. It has power enough. Great in the street or in a noisy jam, but the sound is everythind but sweet and harmonic, I think. Especially the two treble strings sound harsh and kind of muted up the neck and has too little clear fundamentals, but instead a lot of unpleasant overtones, and nail noises, like a cheap guitar and not a beatutiful Martin. The guitar is all solid (spruce and indian rosewood). I have looked inside it, and there is nothing loose. I use GHS vintage bronze 11-50, which sound great on my other guitars. The tap resonance is accvording to my tuner a little below A. I have wondered if the top could be a little too lightlu braced. It has s
Unfortunately it may be just the way that particular guitar sounds. Solid top guitars can have a pretty wide variance on tone from top to top. As the wood ages the tone will also change.
You should check under the saddle and see if it has been shimmed. If the action was lowered and then raised again, a piece of plastic or possibly even cardboard may have been placed under the saddle. A shim can change your tone significantly. If there is a shim, you should have the saddle replaced with a new bone or equivalent material one (not the cheap soft plastic ones).
It is also possible that there was some router "chatter" when the bridge was made and the saddle slot isn't fully flat, causing less than full contact of the saddle bottom to the bridge wood, which would also give you a loss of tone. This is a simple repair for a qualified Luthier.
Sometimes an instrument will sound better under different tensions, so trying out different gauge sets of strings may help. Some guitars will sound better with lower tensions, some with higher, so you will have to do some experimenting. Also check out alternative sets like the Silk and Steels.
Edit: You might also try replacing the bridge pins with wooden (ebony or rosewood) or metal pins for a tone change. The metal ones give more sustain and brightness, but I have heard them give a guitar more "fullness" too.