It wasn't a clone, but rather an attempt to emulate it by making an amalgam of various pokemon traits. It wasn't as perfect as Mewtwo, but the best explanation I can have for it is that they didn't have a solid base. For Mewtwo, they used Mew itself, which is a base for all other pokemon. For Type: Null, they just slapped a bunch of stuff together and hoped it worked. There also seemed to be a different mentality, since Mewtwo is not that far off from Mew. The DNA was changed, but very subtly, to where it would only affect it's capabilities. Type: Null is a more direct melding of traits from several sources. Mewtwo seems more sophisticated in that sense because it implies they figured out how a pokemon's abilities are expressed across several sources and was able to isolate it without anything else being expressed.
Basically, Type: Null was just a sloppier job than the Mewtwo project. I don't know if it was because they had more time or they were able to get better scientists due to having better funding. Whatever the case may be, it was the quality of the project and not what they were trying to emulate that was the reason. Although, I would also imagine if asked to try to make a creature like a mythical being that is all powerful, they wouldn't even know where to begin. You're asking to create something that we don't even know to exist! I suppose with sufficient knowledge of legendaries, one could get close, but you would need to be able to find them, and that should be beyond the capabilities of even the strongest trainers in the world.
