Wow, those 2 games have totally different genres (they are very different). Despite that, I would choose Battalion Wars II over Super Paper Mario any day since it has a greater replay value (online play is great).
Super paper mario is a fun game, took me about 20 hours to play but i havent played battalion wars yet. But super paper mario gets annoying to be and you usally have to use a walkthrough or its impossible but its a very good game atleast rent or buy it ;p