Boarding takes a long time, true.
There are more efficient strategies (.pdf) which have been proven to speed up boarding by between 20% and 50%, still they are not adopted.
Why?
You need to load the baggage, too.
Also the catering.
And fuel.
You need to inspect the aircraft, run through checklists and brief the new crew.
This all takes up time, too.
Airlines do not see a big saving by loading passengers faster, and then waiting for all other jobs to be completed.
Your radical idea of containerizing passenger transport would certainly speed up things, but it would cost a lot of payload.
The most efficient pressure vessel is a sphere, and the next efficient is a cylinder with spherical ends.
Pressurizing a boxy container is structurally very inefficient.
Loading passengers on palettes first and sliding those palettes through a narrow opening takes time in itself.
And the palettes have their own weight, their own floor, their own support structure for the baggage racks, their own cabeling for the entertainment system.
They would, however, not need their independent pressurization, so their weight impact would be moderate.
A possible "flatbed" airliner which could attain the shortest boarding times has only half as much fuselage height (or less) to transmit bending loads along its length.
See here for an example of buckling in a fuselage skin due to bending loads.
Now consider that reducing height by 50% will need four times more cross section in the longerons to keep stiffness constant.
That will make the fuselage much heavier.
In the end, airlines go with the solution which maximizes their profits.
By using a hollow cylinder and let their "cargo" self-load, they can maximize their payload and get tolerable boarding times.
Tolerable for them, that is.
That better loading procedures could allow you to come to the airport later is of no interest to them.
If they would see an advantage in shorter boarding times, there would be ample of opportunity by improving strategies, even with existing airplane designs.
aviation.stackexchange.com/users/1961/Peter Kämpf
The system you propose would be extremely heavy compared to existing aircraft.
More weight means more fuel and more fuel means even more fuel to carry that fuel through the air, and even more fuel to carry that fuel and so on.
Fuel is one of the biggest expenses an airline faces.
It would also be extremely expensive.
To gain any time, you'd have to have the departing passenger capsule loaded and ready before the arriving passengers have left their capsule.
That means you need twice as many capsules as planes.
And the time saving wouldn't be all that great.
You'd still have to refuel the plane and load and unload the cargo.
Manoeuvring a fuselage-sized capsule into the plane would be a long job.
I'm far from convinced that it would be faster than getting however many hundred people through the door.
aviation.stackexchange.com/users/946/David Richerby
The first and biggest concern would be the weight of the container.
They need to have walls, floor and a ceiling and be able to lock in place on the plane.
Also each division between containers would remove some room available for another row of seats in the traditional method.
aviation.stackexchange.com/users/609/ratchet freak
Passenger crates were envisaged a long time ago.
Apart from the above objections, may I add this: A passenger crate in a plane is a box in a box.
This would worsen claustrophobia which is already a problem.
A view outside would alleviate this, but requires windows.
Crate windows would need to be aligned with fuselage portholes.
The psychological problem is doubled by a physical problem which is emergency evacuation.
Any project would need a highly standardised crate compatible with competing aircraft types.
This standard would later become a constraint for future design innovation.
It would also limit customisation of planes by constructors for specific customers.
aviation.stackexchange.com/users/7118/paul_wi11iams
I wouldn't want all of the connections for pressurisation, air conditioning, lighting, water, IFE etc etc connected and disconncted every flight.
A maintenance and safety headache.
aviation.stackexchange.com/users/595/Simon
Something even more radical has been considered!
Airbus filed a patent on replacing the entire upper fuselage - seats, passengers and all - during a layover.
The structural problems inherent in that idea look pretty hard though.
aviation.stackexchange.com/users/13709/FLHerne
My suspicion is that delays in loading passengers onto aeroplanes come from two sources: 1) Security & border concerns since the hijacking of aircraft became common in the 1970s; 2)
Airports' desire to make money from passengers being forced to wait in airports, where they buy things from retailers who are paying tenants of the airport.
On the topic of (2) a British airport group (Heathrow is one of their properties) told shareholders around 15 years ago that they were not in the transport business, but in the retail business, pointing out that over 60% of their revenues came from rents paid by airport retailers.
It's elementary economics that while this is the case, airports and airlines have no incentive to make aircraft boarding quicker, even if a solution for (1) were found.
Were airports to shift their revenue model away from retail, this entails airlines paying more for landing slots, so the two groups have a common interest in wasting the time of travellers by keeping them in airports for as long as possible out of their travel time.
A saner approach to speeding up the loading of passengers would be - rather than loading them in boxes like freight - to simply cut the airport out and have passengers board special buses in town, check their bags and travel documents with a couple of officials who are also travelling on the bus, and have those buses drive straight onto the tarmac and up to the aeroplane.
This is after all how very rich people travel.
Someone drives them straight to the aeroplane.
Airports earning 60% of revenues from in-airport retail tenants are unlikely to support this simple idea, however.
aviation.stackexchange.com/users/7138/Mark Griffith
I for one would jump at the chance to arrive earlier, "board" earlier and sit in cramped airline seating even longer so the airline can save money.
If you didn't pre-load the passengers in your capsules before the plane was ready to depart, there would be no time savings.
No thanks.
It's bad enough they hold you prisoner on the plane when there are hour + long delays in departure.
aviation.stackexchange.com/users/12116/Greg Taylor
Apparently, the time for boarding and deboarding an airplane is a large cost factor and something airlines try to minimize but have trouble controlling because the passengers do it themselves.A solution would be to have passengers board a passenger cabin outside of the airplane and then slide that cabin into the plane via a nose-hatch, much like large volume freight. Has this been considered? If yes, why was it not pursued?
Why don't airlines load their passengers like freight?
aviation.stackexchange.com
<airliner><commercial-aviation><passenger><economics><boarding>
aviation.stackexchange.com/questions/12300
aviation.stackexchange.com/users/935/yippy_yay
Loading passengers in the same way as freight is not really advantageous to airlines. It would not be much faster than current boarding times, the container would add a considerable weight to the aircraft and passengers would possibly suffer greater claustrophobia, which is already a problem during flight.  Although this process might speed up boarding, it could also be quite a time-consuming process in its own right. It would also be very expensive and could significantly increase the weight of the aircraft.  
Although this concept might speed up the process, it would be very expensive. This concept in itself would be time-consuming. The proposed system would be very heavy. This would worsen claustrophobia.