The two cities in the subject line are often spelled Lyons and Marseilles in English. AIUI, they used to be spelled that way in French, too. So somewhere along the line they lost their S’s. But other French cities, such as Paris, Amiens, Reims, Orléans, Tours, Poitiers, Nantes, Chartres, and Rennes, have not. So what happened to Lyon and Marseille? When and how did they become singular?
Who says they are singular? Most of the other names aren’t nouns otherwise. A tour is a tower, but what is a nante?
Hey, I was just being a bit ‘clever’ in calling them singular, impying they were plural before. Don’t take it so serious. Although it is a bit odd how many French cities’ names end with S. I could have easily doubled the length of that list without going to any very small cities.
Nitpick: The S in Reims is pronounced! (I don’t know why it’s so special.)
This can be as much debated among Francophones, equally without clear results:
Whether you pronounce the ‘s’ is the least of the problems when pronouncing ‘Reims’ in English. Pronounce it as the French do and you’ll mostly get blank looks from English speakers. And then there is the issue as to whether in English you spell it with an ‘h’.
There’s a reason Joan of Arc was able to re-capture it. All the orders from the English officers to their soldier got confused in the grapevine !
FWIW, I’ve been to both cities. I don’t recall ever seeing “Lyons” even once (all I remember is horrendous kerning of LYON), but have seen “Marseilles”. Could that city still be in transition of losing the final “s”?
There is also the hotly contested issue of which is France’s second largest city. For actual city, Marseilles, wins, 832,000 to 500,000, but for metro, Lyon wins, 2.2-million to 1.8 million.
Most people will think you are merely clearing your throat.
That’s how the entire French language sounds to this English speaker! 
I was just talking about spelling. French pronunciation is a can of worms I don’t want to open at this time (or pretty much any time, come to think of it).
Marseilles was the Old Occitan (langue d’oc) spelling as found in the original form of the city motto De grands fachs resplend la cioutat de Marseilles (1257). The current Occitan spelling is Marselha. Why it changed I don’t know. Nor do know what the Old French (langue d’oïl) spelling would have been at that time.