I tend to view hotels as the place you sleep, nothing more. You pay for location (i.e. not in the armpit of Shinjuku, for example) and quality, but I've no interest in anything other than clean, with en-suite facilities.
A Ryokan is a good experience (if you get a good Ryokan, of course), but the good ones, as mentioned above, are ludicrously expensive. No matter how many of you you cram into a single room, Ryokan usually charge per person rather than per room.
I get on extremely well with the Chisun Grand in Akasaka. The staff are extremely helpful, they have an entire non-smoking building (the hotel is made up of two physically separate buildings), it's right outside exit 5 of the Akasaka metro station, and the area has some truly glorious restaurants (as well as an open-late bookshop and some 24-hour convenience shops). The rooms are small, but with plenty of space to stash a suitcase where you won't trip over it in the night.
Chisun Grand Akasaka
This time around, though, I'll be giving the Prince in Sunshine City a try. I've heard good things about it, and now that the new metro line is in place Ikebukuro is far more accessible (and the rest of Tokyo is far more accessible from Ikebukuro).
Reviews on Trip Advisor
I don't recall it being a 20 minute walk from Ikebukuro station to Sunshine City, so maybe the reviewer got a bit lost
Be aware that unless you specifically request a double bed you may end up with twin beds. I've spoken to many couples who've complained of sleeping in twin beds in Japan because they never thought to confirm their requirements with their booking agent or the hotel directly.
Japanese hotels are usually for business travellers, so your room is more often than not fully stocked with a fridge, free bottled water, a TV, free internet access (whether wifi or a Cat-5 cable - check first if you intend to use it), toothbrushes, soap, shampoo, disposable razor, comb / brush, toothpaste, shower gel, shower cap, flannel, towels, yukata, slippers, alarm clock and toilet paper. Some hotels also have things like conditioner or moisturiser but that's more dependent on the hotel itself. I've yet to stay at a Japanese hotel which didn't supply all basic toiletries for free, though.
There's little more traditional than pooping on your Toto Washlet and having it wash and air-dry your bum before you have a soak in the bath, wrap yourself in your yukata, and settle on the bed to watch Japanese paparazzi trying to induce epileptic fits in their victims
