for me i'd have to say
-more characters(everyone that was ever in a naruto episode to be exact..that includes narutos mom and kakashi's dad but most of all OBITO plus madara's lil brother)
-as far as your ultimate jutsu id like to be like NSUN4(when loss a certain amount of health your ultimate jutsu changes
-i'd like to add it to were you have summon vs summon (like gambunta vs manda*or whatever his name is*)
-more interactive environments like with the first ultimate ninjas
- and like xShinra Tensei said they should have to were you have to worry about getting hit with a million rasengons
-and they could make it to were you could have 2 ppl at the same time helping each other (kinda like a split screen so they could fight at the same time and help each other. for instance in 2v2
scenerio if your partner won their fight then both of you could beat up on the other guy)
-as far as support goes they could something MvC3 were all support character help you(but it be way better then what they did in storm 2)
-plus they could follow MK a bit and show battle damage plus showing a bit of blood never hurt anybody, i mean look at MK that games F***ING awesome
-one thing id think be cool is if they did a clash mode. ie. in dbzbt1,2&3 and all the others they had it were if you both you and who ever you were fight dashed at each you'd have to spin the analog sticks(the whole time they're moving really fast fighting and all you see is black lines) for a short time and your person had more punches then they'd win. they also had this thing were if you were just fighting and beating the crap out of the other guy then it would show your attacking and the other guy dodge all the attacks and counter at the end.
-and they should add a create a shinobi mode and you could make them look like what ever you wanted to. for me itd be Po frm kung fu panda "skadoosh", that or bruce lee(cuz chuck norris would get crushed plus thet bruce lee kick kick thing is funny as hell)
...i think thats itxd