A Good Game, for Most Part..
The only things I would Tweak would be the Following:
1, to Lengthen the time before the first wave comes in so we have time to set up our first line of Defense;
2, I noticed too that looking at the Stats for upgrading certain Aspects of each weapon, specifically the Reload Time, didn't see a change in the Second-to-last and Last Levels of Upgrade, which makes me feel guilty that I spent the money to upgrade it, but I don't see it, so it seems like that needs to be tweaked.
3, may I suggest instead of an Attack Level for the Ninji, maybe have a Time stat which determines how long they stay attached to the Marios? I think it would make them more useful, in my Opinion.
Otherwise, a sound game, but it needs to be Polished a little bit to make it greater.