As mentioned before me Phione don't evolve into Manaphy due to the possible reason that GAME FREAK wanted to maintain the trend of "Legendary Pokemon not evolving". My answer to your question is a possible reason but is just my personal hypothesis, only GAME FREAK can give you the concluding answer.
To start both Phione and Manaphy are based on marine Gastropods and to be precise the Japanese Clione. Gastropods are considered hermaphrodites thus making them have both female as well as male organs. For a strange reason they still need to mate in order to have offspring. (I am not going to tell you their mating ritual :P). What I will say is that they mate with equivalent species not any other, it must be of the same species, sub family and kind.
Ditto seems to bear some similarities to Gastropod but as a result to what I just said, Ditto is the error link and the reason why Ditto+ Manaphy= Phione. Due to the fact that their adhesive DNA colided and since a seed has both the traits of the mother and father figure (Manaphy and Ditto respectively). Phione share Manaphy's appearance whiles the have Ditto's ability of turning into liquid and taken liquid forms.
As a mutation/clone Phione is notable weaker then Manaphy but stronger then Ditto. If you lookbat it's stats it almost has the average of Manaphy's and Ditto's stats combined
Hope this was of any help