Katamari Damacy.

A fair guess, but not quite. You're reasonably close too, not necessarily due to series or platform in this case, but because the genre is similar to my game (but not exactly) and my game is equally unique.

When I said "beach ball", I literally meant a beach ball. I'll put this up in a second hint;

#13
This game features beach balls collecting things.

Hint 2: And that's just it. It's just a beach ball. A different looking one each level though at least. Besides collecting things, it's jumping from beam to beam and can roll around all sides of such a beam. And oh, this beach ball is directly controlled by the player, it's you.

Hint #12
A Battle between earth and Sea, which was recently remade.

Pokemon ruby/sapphire

Correct but I would prefer if you mentioend emerald as well cause I prefer than one :(

#13 - This game is about fighting 16 consecutive bosses.

Gonna bring this up again, since no one got it.

Hint 12: One of the best RPGs ever on the Dreamcast, it had a fun and interesting battle system that felt very lively. Characters moved on the field when active to attack enemies. If you timed it right, you can cancel your opponent's attacks before they can act. Also, one of the best battle themes ever made.

Ding ding ding!!! : D

Correct.