I would say that we should just live with the difference. There is a near guarantee that our experience of paintings as they exist today will always be significantly different to how they would have been experienced when they had been made, regardless of what we do. The factors are:
- Yellowing of oil/pigment/varnish. This is pretty much inevitable, even in modern paints.
- Fugitive colors. Most high-color pigments tended to fade significantly over time. Degas was once seen crying in front of a Delacroix, upset at how badly the colors had faded, even in his lifetime (It might have been Manet... can't locate the relevant anecdote online).
- Excessive varnishing. It used to be so that paintings received regular varnishing by their owners. Over time, the layers of varnish would build up to a ridiculous degree.
- Lighting. For me this is probably the most annoying factor. A general rule is that paintings should be lighted in the same light that they were painted. The values go to hell if a painting is lighted too brightly. There are many so-called hanging experts, who always light too strongly, even in respected national collections.
Semi-related anecdote: The first time I went to the Rodin museum I was struck by how badly one of the busts had been lighted. Whilst the guards were not looking, I moved it to a more agreeable position. I came back one year later to find it was still in that position.
As for using modern varnishes... I am not expert, but AFAIK one factor that accounts for the amazing longevity of old paintings was the compatibility between their many layers. The canvas, the primer, the paint and the medium were all derived from the same plant: flax. On top of that would sometimes be laid stand oil, again derived from flax. If this continuity is broken, all manner of problems might arise, most of which would be long term issues such as cracking and flaking.