I've stayed at this hotel and the one in Osaka several times and never had any issues, they always recognize my status and give me a free upgrade on arrival (although it's not like you can usually even tell with Ibis). The Kyoto location is brilliant though, you're just across the street from Kyoto station.
I'll be staying at the Ibis Styles at Tokyo Bay soon and noticed they also charge extra for breakfast, and quickly checking the other Styles in Japan they seem to be the same, an extra 1000yen for breakfast service. I suppose the "all-inclusive" plan never went anywhere. Their breakfasts are typical Japanese business hotel fare, probably fine for travelers to Japan or people on business but for those of us who live here or stay in Japan frequently you'd probably be able to get something better outside for the 1000yen.