Hi clara - good idea to stay close to MGA and fly out to the Corn Islands following morning. If you catch the morning flight, and everything runs ok with the boat between islands, you'll be on Little Corn before noon. The dive shops are just off the small town, with numerous places to stay nearby - without needing to go further out on the island, though walking around to all the cheaper places (Elsa's, Grace's, etc.) isn't that far. I recommend booking some place for the first night; spend part of the first day walking around the island to see if there's some place you'd prefer staying.

For Nicaragua, I agree that Ometepe and Leon are the places to explore, with a night to look around Granada maybe in-between. My favorite Pacific beach area is Jiquilillo, but with so much beach time in Corn Islands and Utila, it's probably going to be rather anticlimactic.

It's a long haul, but here's a direct shuttle that will get you from León to La Ceiba for catching the ferry to Utila. I have not used this but done public transportation. If you want to break up the trip using public transportation, I recommend positioning yourself near the border with Honduras around Ocotal on the Nicaragua side. You could potentially visit Somoto Canyon the day before, but you'll want an early start heading to Honduras.

In Tegucigalpa, take a Cristina Bus to La Ceiba. It goes through El Progreso, completely bypassing San Pedro Sula.

Hope this helps with your options; Enjoy ~

Most people would skip Managua and get there urban Nicaragua experience in Leon. Most of Managua is a very modern city, without a lot to offer tourists. From the airport you can get to Granada in 45 minutes by taxi. Or by taxi and collectivo van from the UCA bus place, you can get to Leon in 2.5 hours from the airport.

We are experienced backpackers and prefer some of the ‘off the beaten trail’/less touristic experiences, as may be a possible.

Other than Managua every place you listed is very touristy. Though most of Ometepe is pristine and only lightly touristed. Certainly you should stay away from San Juan del Sur, which is tourist central for Nicaragua. If you want to go a bit off the tourist trail, instead go to the backpacker beach at Jiquilillo, in the northwest. There will be gringos, but very few restaurants, and no shops at all.

Another off the radar region that gets few tourists is the high mountain region in the north, explored from Matagalpa or Jinotega. This is the greenest region of Nicaragua, and only gets a trickle of tourists.

A week for Utila and let's say 4 days for the Corn Islands so 4 weeks left. Minus travel time so just over 3 weeks left maybe? I would spend 10 days or so in Nicaragua and the rest in Guatemala (unless you are planning to go back to Guatemala another time). I like Nicaragua a lot but I love Guatemala. In Nicaragua: Ometepe Island for 3 days, Granada for a day and Leon for 5 days with the overnight volcano Telica camping trip, volcano Cerro Negro, Las Penitas or Jiquilillo for the beach and surfing.

Once you get to Guatemala... if you do end up in Puerto Barrios take a boat to Livingston and then the scenic boat ride to Rio Dulce. It is not my most favorite area but if you are there anyway you might as well see it. Then a bus from Rio Dulce to Flores for Tikal (stay overnight at the park... you can sleep in a hammock or tent in the campground).Even if you are not into Maya temples/ruins I believe you will love Tikal and its rainforest setting and the wildlife. Then a shuttle to Lanquin for Semuc Champey (stepped pools and caves). Shuttle to Antigua. A day in Antigua. Then Lake Atitlan (Maya villages and markets but also great hiking and scenery) and if you still have time Xela (volcano hiking, hot springs) or go back to Antigua for the overnight volcano Acatenango trek. I think you would love Semuc Champey but it does take a whole day to get there and to get from there to Antigua. If you decide to skip it you can take an overnight bus from Flores/Santa Elena to Guatemala City or fly.

Thank you, we thought it might be a bit much. But it looks like we have to skip a few things anyway as there is no boat running between Granada-Ometepe-San Carlos at the moment due to the low water levels if this information is still right? It's on the Ometepe ferry HP. Or are there any locals taking backpacker across on smaller boats?

We are happy to fly between Nicaragua and Guatemala if time gets short. Or even back from Corn Islands.

Since this is your first time in Central America, I agree with #3 and fly in/out of MGA. No sense your initial impressions of Central America be getting from SJO to beginning your time. Even with a late flight, plan to begin in Granada or León just to ease into being there. Plan your itinerary from there based on time and interest(s).

FAVORITES
Food: Anything off a street fritanga with all the grilled meats and side dishes. My favorite is run by sisters, nightly behind the main catedral in León.
Drink: The fresh fruit juices; especially Pitaya and Tamarindo. Great choices at Gordito Kiosko in Granada's Parque Central. Good, inexpensive food too if you can handle all the roving vendors.
Shop: Makeshift gift shop inside León's Museo de la Revolución, across from Parque Central. I've found some very interesting t-shirts, relics, reading things in there over the years. If you've any knowledge or interest of the recent Sandanista-Contra conflict, this is well worth your time if you understand Spanish.
Beach: Jiquilillo; Rancho Esperanza is where one goes to 'check out' for awhile. Incredible sunsets! The longer you stay, the harder it is to leave.
Tradition: Personal, not local, but I try to go volcano boarding every time I'm in León if I've time. Been at least four times, always with Bigfoot.
Hike: I did the overnight hike to Telica when lava was still visible in the crater. Otherwise, I've been up to San Ramón Falls on Ometepe three times.

None of the things you mention are off the beaten path (except maybe Managua). But it is not because these places are not off the beaten path that they are not great. The Corn Islands: you would have to fly there and back and I assume you would want 2-3 full days there so that is already a good chunk of your 13 days. I am not fond of SJDS but you might love it as it sounds like you would enjoy a good party. Be aware that the beach in town is not the best and you will be commuting to the better beaches north and south of SJDS. You could consider Las Penitas instead as it is close to Leon and you will want to go there as it is not only a great colonial city with good nightlife but volcano Cerro Negro (volcano boarding) is a half day trip from Leon as well. A day for Granada would be good with a boat or kayak trip through the isletas and of course active volcano Masaya (your chance to see lava). Ometepe deserves at least 2 full days. 3 days if you want to climb one of the volcanoes (Concepcion is active, Maderas has cloud forest, both are tough). Yes, you can rent a scooter and there is a waterfall (San Ramon). You can't go all the way by scooter though. The last part you have to hike. You can use the scooter to get to the Ojo de Agua natural spring pool. There is also the Charco Verde nature reserve (nice beach) and next door Chico Largo Adventure for ziplining.

With only 13 days I would not be tempted to spend time in Managua but you could spend a day and enjoy the nightlife, I guess.

So you could do this: spend 2 days in Leon (+ Cerro Negro), 1 day Granada and volcano Masaya, 3 days Ometepe, 2 days SJDS, 4-5 days Corn Islands and 1 day for Managua.

If it were my trip I would skip the Corn Islands and I would go to Las Penitas instead of SJDS. Not going to the Corn Islands would give me time for the overnight volcano Telica camping trip (from Leon) and for the Somoto Canyon or nature reserve El Tisey near Esteli (or for hiking around Matagalpa... rafting is possible there as well).

We get around by bus and minibus. You can also take taxis of course.

Do I have enough time at Granada and Leon?

Personally I'd say no, but depends on what your expectations are. You have enough time to visit the central sqares in both towns. depending on your timing you could easily miss the hours when you can go up to the roof of the Leon cathedral to view the volcanoes. You'll only barely be able to scatch the surface in either town. It's not like Granada has only one church to explore. There are plenty. The San Francisco convent in Granada has an especially good museum.

Looks like you've planned almost 3 days for Ometepe, which is good. I'd say use your "open for ideas" days so you have enough time to better see Leon and Granada.