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I was on a flight from Philadelphia (KPHL) to Boston (KBOS), after some delay and some change of route due to weather, the captain announced that we will be cruising at 7000' due to delays in the area.
The history of the flight is here: https://flightaware.com/live/flight/AAL2606/history/20190618/2235Z/KPHL/KBOS
My question is two fold:
The only reason for your flight to operate at such low altitude is because it is cheaper for them to do so.
As you said it is due to weather, other route/altitude may not be available. They can cancel the flight but that is likely to be costly. They may have to find accomodation for you and crew until they can put you to the next flight. Sub-optimal flight maybe better than no flight in this case.
They may need that aircraft at that location the next day. If they choose to cancel your flight today, they will have to find a way to have this aircraft or another aircraft to fill in for the required flight the next day. They might as well fly a slightly more expensive flight at lower altitude rather than fly an empty plane to Boston.
It is possible for them to wait for weather to improve but there is an issue of crew working hour. A pilot cannot work more than 8 hours in a day without provision for additional crew. They may approach that limit and the wait for weather to improve might means the airline has to provide another crew for the flight and might mess up crew schedule for the next few days.
So for the airline, in this case, flying lower and slower maybe a better option for them. Hence higher fuel comsumption is better than no flight.
I used the playback function of Flightradar24 for the 18th at 23:00 UTC, and the amount of traffic above 10,000' (filtering by altitude) seemed very normal compared to other days. I'm baffled as to why they flew so low, but I can address your fuel question in some detail.
The difference in fuel consumption is ~693 kg of fuel, and would cost an extra ~$415, which is certainly not disastrous, but can be a good profit on another short-haul flight (volume economics).
The decision to go ahead and fly low, as has been covered, is not just about fuel. There is a myriad of direct and indirect costs associated with cancelling a flight, and its knock-on effects.
How I arrived at the fuel figure:
The distance flown was ~360 NM (nautical miles). The more direct no-weather route takes 307 NM.
I'm limited by 10,000'/29,000' as the upper/lower limits of low/high cruise figures.
Cruising at a weight of 50 tonnes:
At 10,000' each engine burns 1028 kg/h while doing 280 knots true airspeed (indicated airspeed is 242).
At 29,000' each engine burns 1305 kg/h while doing 462 knots true airspeed.
Now to subtract the distance and fuel used in the climb/descent:
To 10,000' takes 11 NM and 336 kg of fuel (at a brake release weight of 52 tonnes).
To 29,000' takes 66 NM and 970 kg of fuel.
From 10,000' takes 23 NM and burns 48 kg.
From 29,000' takes 64 NM and burns 114 kg.
Total:
For 10,000', that leaves 326 NM of cruise, which would take 2393 kg (two engines). Adding the climb/descent fuel would be a total of 2777 kg (trip fuel).
For 29,000', that leaves 177 NM of cruise (using the shorter distance), which would take 1000 kg (two engines). Adding the climb/descent fuel would be a total of 2084 kg (trip fuel).
Note: spending the shortest time in cruise (a flight that is mostly a climb followed by a few minutes in cruise) is the right strategy for short-haul flights, see: What should be the minimum time spent in cruise (for e.g. a B737)?
It was because they could get there faster on a "TEC route."
IFR flights are subject to congestion management at the ARTCC level, which means they have to wait their turn in line to be allowed into the airspace. That used to be done with holds (and still is in many other countries), but the US will slow down aircraft, reroute them or even delay takeoff to avoid holds, which saves fuel and therefore money. Most likely in this case, they were facing a long wait on the ground due to congestion in ZNY and/or ZBW.
However, if a flight stays low enough, it may be in contact with various TRACON facilities the entire way and never talk to an ARTCC, which means it can avoid the congestion and therefore leave immediately. This typically requires flying below 10k MSL for the entire trip, which is the normal boundary between the two. (It varies between 9k and 12k.) In fact, doing this in the NE US is so common that they've developed an entire suite of preferred Terminal En-route Control (TEC) routes to make it easier for both pilots and controllers.
Using TEC routes burns more fuel because the planes are flying lower and slower than normal, which is inefficient for turbine aircraft, but in some cases the airlines may decide that's better (i.e. less bad) than delaying or canceling a flight.
That’s a typical alternate route to KBOS by sending them direct to FJC VORTAC thence routed eastward. I suspect the real reasons for this are reduction of traffic congestion for NYC arrivals by ATC. On lighter days, they’re typically given the ROBUC3 arrival into KBOS immediately after departure from KPHL.
If they had an issue with the pressurization system, they'd fly that low. Why not cancel the flight? Well, that'd cost money. It'd be cheaper for them to fly low, eat the extra fuel costs and make buck on passenger fare. Who knows, maybe the part needed was nearby so they were going to have to route the plane there anyways.
Possibly, the flight was too dangerous at a high altitude due to complications in weather, and therefore they decided to fly lower and slower. Flying at 7000' is very fuel-consuming, but they could do it since Philadelphia and Boston are fairly close together.
