You can rent a power hammer/scraper and blast all the tile off.
You should be able to get it pretty smooth that way. A good beltsander with some 40/60 grit emery will flatten anything left (use a good respirator).
If it's a small bathroom - it's a lot of work, but doable.
If it were me - I'd take a skilsaw, set the blade to 3/8 depth with a demo blade and criss cross that plywood and just peel it all up.
REAL pain the but - but if you want to to things right and set a floor that'll outlast you, that's the way to go.
Yyou should then use 3/8 cement board set in thinset - tape the seams.
whatever you do, remember floor height is important - don't do the 1/4" on top of the 3/8 plywood. 1/4" doesn't sound like a lot - but it is. The floor will look and feel real thick.
Do it right.