It was an awful, AWFUL spinoff title, but I think a Pokemon Conquest anime adaptation would be absolutely fantastic. The Sengoku Musuo animation, whilst pretty slow and nowhere near as good as Sengoku Basara, wasn't that badly done, and I'd love to see Conquest done in this style. Considering all the Legendary Pokemon floating around in that game it could have some fantastic battles, too.
A proper adaptation of Red's journey would be great, too. As nice as Pokemon Origins was, it was too short and focused on the wrong things, it didn't do itself justice.
Also, I really want a spinoff series that focuses on the better Characters of the Day that have cropped up over the years. I want to see what happened to Giselle after she quit the school, if Seymour the Scientist is still living with the Clefairy, etc etc. Most of the COTD have been forgettable, but there have been several over the years and over every series that warrant a second look. Same goes for the rivals and travelling companions that have fallen by the wayside, too.