There is no fine print worth speaking of. In general it's not very hard to find seats (except at peak times - the day before New Years etc.). Honestly, we're talking about reserving a seat on a train, not getting an approval for a mortgage.

OP just needs to go to the JR travel desk at NRT and request his ticket to Kyoto. The people there will sort him out with reservations. (In the event they inform him that there are no reserved seats available, then it's true he would do best to change at Tokyo, where he has a chance of picking an unreserved seat. This sometimes happens at peak travel times. However, it's typically quite easy to get a seat reservation).

Pure fantasy.

There is no cap on the number of reserved seats per train. Any open reserved seat is available to holders of JR passes.

I think it is the EuroPass (though I'm not sure) one of the European Rail Passes or trains where caps are put on the number of pass holders per train, though I am not too sure on the details.

The JR Pass has no such restrictions.

just curious then...if there are no caps on reserved seats, then why am i told there are no more seats for reservation and then get a seat on the train with many empty seats around me? (not out of Shinagawa)

I suggest this question belongs on another thread. (Also, you'd need to offer more detail about the situation for anyone to make a sensible suggestion as to why it happened).

I have been the evil guy for numerous times

1. Due to scheldue change, I ended up taking earlier / later train, which I dump my reserved seat ticket / change it at those machines
2. reserved more than 1 reserved seat ticket for same direction train due to unconfirmed scheldue, dumping one of them without canceling (applies when I travel on JR Pass)

And I think it's something to do with the reservation system restriction also.

Why Shinagawa? Isn't NEX to Tokyo both faster and more frequent?

Change at Shinagawa because

1. The frequency is the same, Any NEX stops at Tokyo will stops at Shinagawa anyway, and all Tokaido Shikansen stops at Shinagawa as well (don't to be mis-lead by the JR time table, they are actually 1 train split at Tokyo station, heading Shinjuku and Yokohama afterwards)

2. Tokyo station is bit more difficult to navigate (especially for 1st timer), and for NEX you climb for B5/F to 2/F for Shikansen, versus the relative simple Shinagawa Station Layout. Of course if you are going north of Japan, change at Tokyo station instead.

Map for Tokyo Station
http://www.jreast.co.jp/estation/stations/1039.html

Map for Shinagawa Station
http://www.jreast.co.jp/estation/stations/788.html

N'EX typically takes 9 minutes to go from Tokyo to Shinagawa.
Shinkansen trains typically take 6 minutes.
(based on a single comparison of the timetable at about 10am on a regular weekday)

So ... In theory, you might be able to catch a Shinkansen train at Tokyo that you would miss by continuing on the N'EX to Shinagawa. However, unless your name is Usain Bolt, and a path through the crowds at Tokyo station has been specially cleared for this experimental run, you're unlikely to make that connection at Tokyo station.

I haven't compared N'EX arrival times to Shinkansen departure times, so I'm not even sure if this edge case actually exists... but it might.

For those of us who arent olympic athletes, the change at Shinagawa is a good bet.

lol, the Tokyo station map is crazy!

I'm still amazed at the complexity of the Tokyo subway map.
Took me quite a while to figure it out the first few times I used the subway there.

bad boy...

I think what he was trying to say is that there is no cap on holders of JR passes getting reserved seats among the seats available for reservation. Each car on the Shinkansen (at least on the Tokaido line) is designated as "reserved" or "non-reserved." If you try to book a reserved seat and are told none are available, this doesn't speak one way or the other to what's going on in the non-reserved cars. So if you board the train on which you could not get a seat reservation and sit in a non-reserved seating car, it may indeed be empty or nearly so, although this would seem unusual to me as there are usually enough people with regular tickets that don't want to pay the 500 yen fee for a seat reservation that such an imbalance is rare.

Another thing to consider if you happened to squat in a reserved car, or even just observing in a non-reserved car, is that "fully booked" means for the entirety of your journey, not just when you start out in Tokyo. For example, let's say you're going from Tokyo to Shin-Osaka. An answer of "no reserved seats available" means that there is not a seat that's open all the way between the two stations, not that all will fill up at Tokyo. Conceivably, the reserved cars could be completely empty most of the way, then fill up at Kyoto for the final segment to Shin-Osaka, and they'd be "sold out" when you asked for a Tokyo to Shin-Osaka seat reservation.

And there seems to be no limit to the number of people who are allowed to cram into a non-reserved car. Standing in the aisles is permitted and frequently seen during peak travel times.

Or a reserved car for that matter. I've been on a Shinkansen with a reserved seat, only to have the aisles fill up completely with standing passengers. Fortunately, I got on at the terminus and went to the other terminus. I can't imagine how someone with a reserved seat that got on after the aisle filled up would ever get to their seat.

I took the Skyliner from Nippori yesterday. They turn on a front view camera over the last stretch towards Narita and it is really moving fast. But the few additional stations to get to Nippori from the south really negated the time savings. One train every 20 minutes schedule is better than the 30 minutes NEX schedule.

I meant to take 14:05 train but the counter gave me a 13:05 ticket. When I went back an hour later, past the 13:05 departure time, counter charged me Y1200 for the change.

1 train every 20 mins would be better. Unfortunately, there are only 2 skyliners/hour -- the same as NEx. Each hour, it's 20 mins between Skyliner 1 and V2, but 40 mins between Skyliner 2 & Skyliner 3.