OK, it's your trip. Just consider...
Look at the cost to fly to/from a major European hub (London, Paris, Madrid, Amsterdam, Frankfort - pretty much any major city) - that'll be a LOT less than $2000, unless you're really doing something wrong. Then add a hundred bucks (each way) to that (ballpark estimate of a flight between that city to/from Marrakech or Fes). Compare that with what you're considering paying to fly from NYC. I think you will find the difference in cost is pretty dramatic.
Long layover in Europe? Not sure what living in NYC has to do with that, but, you can easily avoid that with just a tiny bit of effort doing some planning. If you just plug NYC-Morocco into an airline's website, well of course that's going to result in useless/insane routings. You do NOT want to fly all that route on one airline or one ticket. Fly to Europe (find your best deal for that). Then, separately, get a cheap ticket from that major hub to Morocco (no airline is going to make that easy for you, it's not in their interest - they would rather charge you an extra $2000 and punish you for asking by routing you through four stops in Uzbekistan...).
From JFK or EWR, you have a nearly endless choice of reasonably-priced flights to any major city in Europe pretty much every day (lucky you - pity those of us on the west coast, or in the middle, if you want to grouse about prices or layovers...). Figure out the cheap ways to get from one of those cities to/from Morocco (flights under $100 if you play your cards right - I paid about $75 from Madrid). Book a nonstop flight to/from JFK/EWR that aligns with the low cost connection to Morocco. I don't know about you, but I would gladly suffer a few hours in some major European airport to save several thousand dollars. Note that you will have to figure this stuff out, no travel agent or airline agent is going to do it for you, but it's quite simple and all the information you need is very readily available if you have an internet connection and make a small effort. Spend an hour with Google, save thousands...or just call United/Delta/American and say "get me to Casablanca" and take what they offer you...it's a choice you make (consciously or otherwise).
As for Fes versus Marrakech, both have their charms, and either one will be a real eye-opener. Marrakech is a little more touristy, Fes is a bit less tidy and more authentic (ratio of ATMs to amount of donkey poo you will need to step over...). Fes is probably a little more, um...intense. If you're at all skittish about the whole Africa/Islamic/develoiping-country thing, Marrakech is probably more accessible. If you're ready to toss caution to the winds, I'd suggest you close your eye and dive into Fes. Regardless, if going from either one of them overland to the desert (a very long day spent driving from either), you will have options for interesting stuff on the way. If going from Fes, try to make at least a brief stop at Todra Gorge. If going from Marrakech, try to stop at Ait Benhaddou, near Ourzazatte. Both are worthwhile. If you don't believe me, just google images from them, I think you would find both interesting.
Your French will serve you well. Getting lost in the medina is a given, you will enjoy it. BTW, I was 100% serious about bringing a small compass, it's very useful in staying oriented and navigating the medinas (although navigating by the stacks of sheeps' heads also works, and appears a little less weird to the locals...). If you go to Fes, be sure to include a visit to the tanneries (but don't do that right after you've eaten a large meal...).
مع السلامة and بالتوفيق
(farewell, and good luck!)