Especially if you want other people on the Internet to play this, you're gonna have to do something about the graphics. I don't know how much time you're willing to invest, but turning the red tunic sprites green is not difficult. Either open it in paint and use the bucket tool, or download gimp (which is free), and use the color exchange tool to change the red to green. Also, I think it would be a great idea for you to play a Zelda game that uses the tiles you're using, either Minish cap and LTTP, or else some fan games, and take time to learn how the tiles you're using fit together. Or just look at some screen shots. But things like three fourths of a tree do not look good and are distracting, and I'm not entirely sure why you used what appears to be the corner of a cliff or something as grass.
Personally, I would also recommend ditching the RTP graphics for the most part, too, but again, that depends on how much time you're willing to put into this. If you're just doing a little game for fun for yourself, and you don't expect anybody else to play it besides maybe your friends, then you can go ahead with what you're doing. But if you want people on the Internet to help you with graphics and stuff, it might be a good idea to study other games, particularly their graphical style. If this is your first game, though, I bet you'll definitely learn a lot, but I wouldn't start with a game as ambitious as this sounds, it will be a little boring. Starting games should be small and easy to finish, I've learned from experience, you'll learn more that way and have more freedom.
Also, I've worked with rm2k3 for more years than I care to count, so if you have any questions pertaining to that, I can probably help. But what on earth do you mean about those clock town sprites? If not building clock town in 2d (such as Minish cap) sprites, what do you mean by 2d Majora's mask sprites?