I played through twice, and on the second time I noticed that the seed count did not reset so I start with about 37 seeds. I found all 40 seeds (it's 40 right?) on my second time through, but it did not give me the "Happy End".
You could also edit the Achievement screen. Why have the scroll to see one more achievement when you could stretch the box vertically to show all of the achievements at once?
On the third chapter the sub started moving a lot faster. Why not set it to that speed for the entire game?