The quotes below are from this link.
http://nymag.com/news/9-11/10th-anniversary/planes/

The first plane.
“The plane made daily flights between Boston and Los Angeles,...”

The second plane.
“Like American Airlines 11, it was scheduled to fly between Logan and LAX.”

According to the above statements, these were DIRECT flights with no stops.

The distance between Boston and New York is 190 miles.

The main question is, WHAT WERE THOSE PLANES DOING AT 1000' HEIGHT IN NEW YORK, 190 MILES FROM THEIR TAKEOFF POINT AND IN SWW DIRECTION, NOT IN WESTERN DIRECTION?!
Going in a SWW direction from Boston to Los Angeles is OFF COURSE! On the map, anyway.

Didn't the passengers notice the planes were descending and more importantly why?

IF the planes were scheduled to stop in New York, didn't the passengers notice the planes were going a little to fast for landing at 440-540 miles/hr?

IF the planes were OFF COURSE, didn't the ATC notice it and if they did notice, why didn't they take proper measures to solve the problem?
Didn't the ATC notice the planes were descending way too fast, IF they were scheduled landings in New York?

When a jet takes off, it is up to its operational height in a few minutes and I assume they climb at about 2000ft/m.
If the plane climbs at 2000ft/m, it will be up at 30,000feet height in 15 minutes.
It arrives 190 miles away in about 35-45 minutes travelling at 440-540 miles/hr. It is not economical to use jets for such short distances.

Jets start to descend and reduce speed, about fifty miles away from their destination.

Did the passengers knew the planes were hijacked (IF they were) by people with box cutters and they did nothing?

If somebody threatens with a knife, all you have to do is get some blankets or clothing and throw them at the mf then half a dozen people could sit on the individual.

As usual with status quo explanations, “The equation doesn't balance”. As a matter of fact, it not only “smells”, IT “STINKS” to high heavens!