All of Arjen's albums have his trademark elements (to varying degrees), sure, but I disagree they are too similar, especially in the case of Theory of Everything. The structure of the songs on TTOE (with songs I mean the parts of the 4 larger songs), the contributions of several intstumentalists and the very distinct and relatively small cast of vocalists make the album quite a bit different when taken as a whole. For me at least. And the story has a noticable different feel to it as well. 01011001 does feel a bit more by the books than his other works, and it has several vocalists with similar qualities. But given it is kind of the climax of his first Ayreon storyline, I feel that approach worked. By no means I would call the album a rehash of the preceding Ayreon albums. The Gentle Storm's more folksy direction with the lack of synthesizers (often a huge part of his sound) also make it quite different for me as well, particularly the Gentle version.
To me, these similar musical elements are what makes his sound, just like I can recognize any of my favourite artists based on certain elements that are present troughout their discography.