Felik is a great game designer and an awesome level layout desiner. I aways said this, and I usually suggest people to play his fangame if they want good leads on how to properly design the layout of a level. Flooded Captal is the pure reflex of this sentiment, though Sparkling Complex have a special place in my heart. =P
That been said, with all honesty, I'm currently not very happy with the direction you are taking your project recently. It seems you are unsure of what direction to put it, and make of it a huge mess of different style, leaving the game without an own identity. And now it seems it is reaching the actual level art of the game as well. As noted by Polygon Jim in the above post, there's a huge clash of styles.
I'll say this because most of the people here at Retro aren't as familiar with this project as I am, that have been following it since the early development of the project. Your project is have a good concept since the begining. When I first heard the name "Sonic Fusion," I realized it had this name because it was a Sonic game made on Multimedia Fusion, but in the same extent as "Sonic Advance" is a Sonic game made for the Game Boy Advance. Do you get what I'm saying? When I actuallt played it, I loved it so much, because you were taking a "Sonic Advance" approach with the project. Even the musics and sound effects were straightly ripped from the Advance and Rush series. Despite the name, Sonic Fusion was the espiritual successor of the "Advance" series. But that is not what made Sonic Fusion so great back then; it was the fact that the game had it's own identity. And that particular identity is what previously made Sonic Fusion one of the better featured SAGE games. Even the fact that you actually toned down some modern musics in order to make they sound as if coming out from a GBA emulator. These all were nice touches. But over time, you seemed to be trying to change the paradigm; you started changing the sound effects to the ones of Sonic Adventure, changing music, game style, and that particular identity that made this game so great begun to fade, to the point that now, Sonic Fusion just looks as good as any other fan game out there (that, despite your own creative gimmicks and incomparable level layouts).
Now, I can't even understand what leads you want to take in this game at all! An this is really uncomfortable, because it appears you are doing the absolute polar opposite of what you were doing in the begining.
Note, however, that I said all of this not to criticize, but instead, as a way of showing what is going on with this project over the years, so you can once again define an identity to Sonic Fusion, and improve it at the best of your abilities. Because this is a project that I like a lot, and I want to see it being executedly as good as possible.
About the anime intro, the menus and cutscenes, they are great! But the sound effects are still way too modern-ishy, and with Sonic Adventure's player select music, well, they all doesn't go along very well. There's definitely a clash of styles.