well, comfort is pretty subjective. imho, i'm more comfortable flying this leg of the journey with a toddler in tow. btw, my reply tends to be more skewed towards travel with young children.
comfort in terms of seat size and space, undoubtedly the trains win hands down, unless you fly top class.
i just realised that i only take trains while on holidays and holidays ought to be less stressful (haha...never in reality!) now train travel in japan can be confusing for foreign travellers. so many platforms, so many trains...it can be very intimidating for foreigners not familiar with the japanese language, and worst if carrying lots of baggage. Add in kids, disagreeable kids, this just makes it a nightmare to travel!
just in april, my partner and i couldn't find our near platform 11 locker in shinjuku train station. hubby was brilliant in suggesting the use of a locker for stashing our shopping loot before our next shopping stop. it made sense since we'd have to return to shinjuku where we stayed. we forget that 1. we wouldn't be returning via the same platform - no big problem, since we made sure to remember the platform number, 2. we wouldn't be using the same exit stairs! (there're stairs in the two ends and also in the middle!) so we spent 20 mins going up and down stairs to find our locker! haha! silly!
to me, air travel is straightforward. it's the same procedure everywhere. just check in, go to gate, get on. and if there's an empty seat next to you, great! your kid can have a seat. nobody's going to board the plane in the next hour to possibly claim the seat your kid is on.
as for luggages and strollers, train travel is pretty much diy. you'll have to load and unload everything by yourself. this means that your partner will have to juggle 2 kids down the train while you ensure you've got everything up and down the train. honestly, that's a huge hassle to me. if you're travelling light, then this shouldn't be much of an issue. we do suffer from certain amount of anxiety about missing our stops etc. but it's just us. there're announcements about the next stops. but if you're the type who may fall deep asleep (not sure how with kids around :P), you run the danger of missing your stop.
an hour of air travel vs 3 hours of train travel is also preferable to me cos it passes quite fast. what more, kids get to choose from a basketful of free toys/ souvenirs inflight. this should occupy the kids for a while. in no time, you've arrived. train travel can get quite monotonous. scenery gets bleah after a while. if you have kids who take 2h naps mid day, then carefully-planned train travel may work for you.
my child did not have to buy an airticket when she was 45months, but i'm not exactly sure what's the cut-off age. for trains, kids under 6 travel free but on your lap or in your seat (meaning, you'll have to stand if your child insists on sitting on his/her own)
i haven't travelled during peak season, so the planes were never full. in fact, i recall vaguely that we were early for one flight and they gladly moved us to the next available flight.
about bad weather, i'm sorry i've no idea, perhaps locals may know better. but it's definitely good idea to avoid any travel during bad weather seasons especially with kids.
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