Travelling to Japan beginning of March (Air Can sale $859 round trip from YEG!), looking for beautiful and affordable hotel or ryokan recommendations for Tokyo and Kyoto. Also looking for suggestions on cheapest way to travel between Tokyo and Kyoto - currently considering rail pass, or perhaps flight from Tokyo to Osaka and an hour bus/train to Kyoto.

Hi!
I found hostels a great cheap option during my time in Japan. I had good experiences with the khaosan chain.
If Kyoto is the only place you will be besides Tokyo then the rail pass isn't a big value. I always just walked on without reserved seats and had no difficulties (I went at a similar time of year).

http://www.hyperdia.com/en/ was what I used to plan my train travel. Accurate and easy to use.
Also consider a day trip to nikko from Tokyo if you have time.

Awesome! Thank you!

Train all the way - easy and fast, and I echo what is said above. Hyperdia will tell you prices.

Kaitlin when you say you just walked on without reserved seats, did you mean you would just go to the station and purchase a ticket there for right then?

We had the rail.pass cause I was there for a month. But essentially yes. You can reserve a seat on trains but I never found it mattered. There was always plenty of room on my travels!

Also just want to add that train from Umeda in Osaka to Kyoto station is only 30 mins if you take the Rapid Express. Osaka has a better night life and is cheaper to stay in. If you want the ryokan experience, stay in one for a night in Kyoto and the rest in Osaka to save money. Just my opinion.

Peach Airlines has cheap flights between Narita and Kansai Airport. Then get the cheap tourist special price for the express train to Kyoto. Please note that when we went a couple years ago this was a cash only deal (no credit cards allowed when buying this pass).
http://www.westjr.co.jp/global/en/ticket/icoca-haruka/

Jhoudiey Lynn
Depending on your budget, Ryokan aren't exactly affordable. Most are about ~300/night, though you can usually find hotels that have the baths and such on the roof as well. The Dormy Inn Premium in Kyoto is quite nice with excellent breakfast and it's like... half a block from Kyoto station.
Travelling between Kyoto/Tokyo can be pretty expensive, I think it's like... $290 for a 7 day rail pass? That being said, it's about $135ish each way for the bullet train, so it may make sense on if you planned on using it otherwise. Keep in mind you cannot buy the rail pass once you're in Japan and have to order it and get the exchange order mailed to your house to exchange at the airport when you arrive. I'm not sure the cost of flights as I've never flown between cities, but usually getting to/from the airports is about $40 anyway so it may even out.
I've been to Japan 4 times now, and am planning the 5th trip this June, feel free to PM if you've got other questions too

My husband and stayed in Kinoe ryokan last year in Kyoto. One of the staff named Khoji was most helpful man and helped us with restaurant reservations for restaurants and to navigate the city bus system. Definitely recommend train travel between Tokyo and Kyoto.

we took the mid night bus from Tokyo to Kyoto and back, is half of the price of the train, and you can save 2 nights hotel money
is not the most comfortable, it will be better if you can sleep in the bus. but is the cheaper way for sure!