Haneda or Narita ?
 

Flight cost is slightly higher for H but is it worth it not to deal with train and tickets as we did last time at N

That's really up to you.

If we're looking at it purely from a public transit access perspective, my opinion is that transit from Haneda tends to be a bit crowded on both the monorail and the Keikyu Line. From Narita, it is a little bit longer, but the Narita Express or the Skyliner are more comfortable. You'll be dealing with trains and tickets either way. Similar story if you take a Limousine Bus.

However from Haneda, a taxi also becomes a viable option if you'll be staying in Tokyo proper. You won't be paying as outrageous a fare compared to trying to get a taxi from Narita to Tokyo.

If you plan to take the Limo Bus to your hotel, check the schedules for both airports. There can be big differences in frequencies as well as a few hotels that are only served from one airport.

Taxi into Tokyo from HND is pleasant, and not unreasonable - especially if you're sharing with others. That said, regardless of how you choose to get into town, it's worth learning how to deal painlessly with trains and tickets. I'm wondering why you found it to be such a chore - perhaps you had to join a line to validate a JR pass or reach the ticket counter?

I usually use HND but flew into NRT for the first time in a while last weekend, on a Saturday afternoon. The train stations at T2 were mobbed and there were crazy lines for the ticket machines. Like a wise local, I entered with my Suica and bought a ticketless NEX reservation on eki-net, so didn't have to wait in line, but even just getting around the hordes of tourists blocking the gates and the platforms was a bit of a challenge, especially with luggage. NRT was not like this a couple of years ago when I would just walk up, buy a NEX or Skyliner ticket, and go.

That said, I have also encountered 100-deep lines for taxis at HND T3. Uber is an effective solution in such cases.

Is there a step by step guide for using the Eki-net IOS app to get the seat reservation fee paid? It's confusing for two passengers, one with mobile SUICA and one with mobile PASMO on how to handle the seat reservation fee on the app for both - although my understanding is one is detached from the other, the SUICA just gives you access to the train and the conductor doesn't see that, but the seat reservation confirmation is what they see on their tablet as they walk through the train.

Is the total cost (SUICA + seat fee) more expensive vs just buying a paper ticket? We can't do the discount round trip (AFAIK) because we are buying the first leg to NRT and the second leg is from NRT instead of the reverse.

I just want to figure out how to avoid that mob at the train station - I've seen it before and it's insanity.

Your understanding is basically right. If you go to https://www.eki-net.com/en/jreast-tr...tion/top/Index and choose the "purchase a ticket" option, it will let you search for the stations and date/time you want. Then it will give you the option to either buy a paper ticket (which you will have to pick up at the station), or buy an e-ticket (which has to be used in conjunction with a Pasmo/Suica). If you choose the latter, you enter the station with your respective Suica/Pasmo cards (whether physical or in a phone/watch), then the base fare will be paid from the Suica/Pasmo and the express supplement and seat fee will be charged to the credit card registered with Eki-net. You can buy multiple e-tickets at once and none of them will be linked to any particular Suica/Pasmo, so you could also buy a paper ticket from the ticket machine for the base fare and use that to get into the station, or borrow someone else's transit card, etc. It is slightly cheaper to use the e-ticket option, but only by like 100 yen each way. They have some even cheaper tickets that are 35% off the usual express/seat fee, but I believe those are only sold through the Japanese version of eki-net.

Keisei also has a very similar (but completely separate) service for booking Skyliner e-tickets online.

There's a lot of factors in there - not least, where in the city are you going to, and how are you planning on getting there.

If you want proximity and are planning on getting a taxi, HND is a no-brainer.

However, if you're planning on getting the train, it's less clear cut, and the ease of doing so depends on the day of the week and time of day as much as anything else, as well as where in Tokyo you're trying to get to. The Keikyu line from HND is great for Shinagawa, where it magically transforms into a metro train in a puff of smoke. But it can be standing room only from T3. The monorail is quieter in the morning, and great for the bay as well as the eastern side of the Yamanote Line (and it's much more fun) but the queues for it in the late afternoon can be horrendous.

OTOH, from NRT you have the Narita Express, which aims to give you as scenic a tour of Chiba prefecture as possible, before doing a circuit of the city's least accessible underground platforms (albeit in very convenient stations). The advantage, particularly if you just want a snooze and to decompress after a flight, is that it's direct to a number of stations on the West Side (does hand gesture). But it's certainly not fast. However, there's also its relative upstart cousin, the Keisei Skyliner, which is pretty fast if you're trying to get to the eastern or northern side of the city - with stops at Nippori and Ueno (as well as the slower, but very convenient SkyAccess line into Oshiage and Asakusa).

If you're doing these - with the possible exception of the Narita Express, I'd also urge you to seek out same day luggage transfer (unless you're arriving in the evening). Yamato, JALABC, Airporter, Ecbo - they are all there to make your life easier. Don't put your back out carrying two massive suitcases up a huge staircase at Asakusa metro station because you're too jetlagged to find the lift and spend the rest of the trip making yourself look very odd by doing neck cracks and shoulder exercises while sitting down for a coffee, having just endured a jetlagged commuter train journey where you've just inadvertently got in everybody's way.

I chose Narita and a taxi to the hotel and I am very glad I did.

All other things being equal, and assuming that you were heading to central Tokyo, I guess you might have been even gladder if you had been able to take the taxi from HND and pocket the $100 difference in fare.

I'd need more info if OP as asking us a suggestion for their trip, but I probably couldn't care less for my own trips.
I usually have a choice of getting into Narita in mid-afternoon or 9pm to Haneda on my usual TPAC flights. 99% of my trips have me connecting to Hokkaido via Haneda and the last plane to Kushiro is 5pm ish. I would never make it there on time, so it's an overnight in the Excel Tokyu or Villa Fontaine anyways.

FT JP threads tend to mention arrivals into Japan more. You might be able to book open jaw or effectively TYO. I'm actually able to choose arrival to NRT and dept from HND or vice versa on the same airline/alliance for my pairings. Sometimes if I have a bit of luck, HND r/t is $100-200 more than NRT + transportation but if that's rather pricey, sometimes I can find a decent deal on arriving to NRT and dept from HND.

I prefer departure from HND to make good use of the last day with late afternoon departure and options for getting excessive consumption purchases to the airport on the same day (namely affordable taxi). I also prefer some of airside souvenir snack shops at HND over NRT as I feel the selection and checkout speed is better.

But that line usually moves fairly quickly, even when it wraps around past the curb next to the building.

I fly to japan 2-4x / yeah and prefer HND.

Oops, I meant to write Haneda not Narita. Sorry about that. I flew into Haneda and took a taxi. I pre booked the taxi on booking.com and it was about $70 US as I remember. It was around 4pm and after a very long flight I considered it money well spent.

I'm just glad that option is there. One trip I was trying to figure out how to get to the Prince Park Tower from NRT after a TPAC flight and settled on taking the NEX to Tokyo station and picking up a taxi from there rather than try and navigate a transfer and walking a km or two with luggage while half asleep.
Once I was rested and needed to head to HND two days later, I chose to walk to Hamamatsucho for the monorail.