This sort of falls into the "just for fun" category, but I have always enjoyed browsing the listings on Jalan.net's "room and two meals for 9800 yen" feature. Given the current state of the travel industry in Japan, you really can't use it as a basis for planning future trips, of course, and I am absolutely NOT a proponent of trying to book rooms in Japanese if you don't have reasonable reading proficiency in Japanese. But it's kind of fun to click around. (Note that not all of the plans listed will include an en suite bathroom.)
https://www.jalan.net/theme/price/price_9800.html?ctm=N11I don't see any point in arguing about the meaning of the word ryokan, as it can be taken broadly or narrowly. To many people, it implies Japanese-style accommodations and meals in sort of a resort-like atmosphere, and some purists even sneer at the notion of including reinforced-concrete high-rise buildings in that definition. But many lodging facilities that are more "basic" can and do call themselves ryokans. Typically they would have tatami-mat style rooms and not beds. At any rate, it doesn't look like the OP is particularly seeking out Japanese-style accommodations for the experience of sleeping on a floor with futons. He just wants more space in the room, and this is more easily obtained when the floor isn't taken up with western-style beds.
I have many years of experience seeking out decent-sized (at least 24 square meters, sometimes as large as 40 or more square meters) western-style hotel rooms for two at a price under 15,000 in the Tokyo metro area. Many of these include a simple breakfast (but not dinner). If you're willing to go up to 20,000 per night, you can often get really nice 4-star hotel rooms on sale (generally without any meals). Spacious rooms in this price range have gotten somewhat harder to find over time, but plenty of them still exist, especially if you don't include a Saturday in the stay. (Years ago, Saturdays used to be a bargain night at business hotels and you could get their largest rooms for a song! Not anymore...) But I really can't see any point in seriously searching at the present time, as room rates are going to change drastically once Japan opens up to foreign tourists. As for staying outside of Tokyo to save money and then commuting, the time and cost issues more or less rule this out. I've stayed at the four-star properties on Odaiba a few times (for around 15,000 yen for two) and also in Yokohama at Minato Mirai, for terrific prices. But my favorite Tokyo hotels are closer in.
I personally prefer hotels with a daiyokujo (aka "public bath" or sometimes called a "spa"), but these are harder to find in Tokyo and I usually get my bathing fix in other regions. Besides Dormy Inn there are a fair number of chains that feature them in all their properties, as well as some individual (non-chain) properties that happen to have one. I have stayed at quite a few Dormy Inn hotels and thought some were excellent but some were so-so. (Dormy Inn is very opportunistic in its pricing and I have ruled it out many times because they were way too expensive, especially when I included a Saturday in the stay. One plus for the chain is that their breakfast is generally quite good and worth the price they charge for it if you don't book a stay plan that includes breakfast.)
I have stayed at a number of really wonderful Japanese ryokans and family-run non-chain hotels that had hot spring baths and two excellent meals for 10,000 per person (in some cases as low as 8000 or less, although that was generally some years in the past), but none of them were in the Tokyo metro area. I think it's best to experience these in the hinterlands, and focus your efforts on hunting for bargains on western-style hotels when you are in Tokyo, is my advice. There are always bargains to be had...