Now, if you're not a tourist passing by for 3 days, Suica has most of your gripes solved and is an incredibly useful general payment mean. I use the Felica version on my phone (so no card), charge it with 3 taps in the app from my credit card, could have it auto charge if I really wanted to and is my payment choice wherever QR codes or QuickPay won't cut it.
BTW you can now use your credit card to ride JR trains.