Has the old flagstone already been cleaned? It could be that the new just needs time to weather. FWIW: My neighbor just had a section of their aggregate driveway replaced and it is much lighter than the rest, but it’ll eventually get just as dirty so it’ll blend. ;)

Thanks for your reply! This has actually looked this terrible for 3 years, we are just getting to fixing it now, so both old and new stones are dirty...

I would clean the old stone more often than the new, so that new stone can catch up in terms of wear. It will. If perchance installer sealed new stone, sealer will delay wear (as a sealer is supposed to do). But even so, sealers break down and it gives new stone time to catch up. Once the difference is minimal, you do need to follow recommended stone care program religiously and for all of the stone area.

I see some greyish flagstone, blond flagstone and some dark flagstone. Only the dark seems disturbing enough to care about. The grey and the blond seem generally compatible and not enough to worry about. Look around Europe, some other old places and Disneyworld. You'll see all kinds of patched in paving that is the result from centuries of fixing and patching things. (In the case of Disneyworld, it's a purposeful attempt to re-create the centuries old distressed look.) The look can be very charming.

Now in the case of the very dark pavers, they seem out of place. You're asking for a cheap solution. I would go to Home Depot or such and by a small box of tile grout, matching as near as possibly the grey scheme, which is the majority color in your photograph. I would mix a thin wash of the grout and carefully paint the dark stone with it, not splattering the solution on the surrounding stones. You could also work with wet stone and sporadic sprinkling of dry grout. This is experimental so don't blame me if it doesn't work. And go lightly at the beginning in order to get a feel for what the result will be prior to going whole hog. I would try a sample in an unimportant area first. The fact is, a wash of grout would definitely stain an masonry product if it spilled on it. I'm just suggesting this staining possibility may be worked to your advantage if you are careful about it. Can't say how long it would last, but while everything is gradually weathering (and changing) you might be able to get a result that satisfies the worry you have now.

Take some dirty water put in on the new stone-honestly-we've done this on tile replacement in a commercial pool patio where the original white grout was a bit dingy. A little dirty water over the new fresh grout stood out less.