@Dave - yeah penalties can be hard to come back from. Google places so much emphasis on signals of trust that once you break that trust you have to do a lot to earn it back. I'm looking forward to more emphasis being placed on content again too. Not the add one more tag kind of thing, but placing the emphasis on content people actually enjoy and revisit. I have a hard time seeing links going away. There are good reasons for using links, but somewhere along the line too much emphasis was given to them.
@Rudy - I think all the things you mentioned play a part. To me the whole "in at the start" thing is about understanding your general marketing as early as possible. Some people will create a product that no one really wants. A little marketing research could have saved a lot of time.
But I do also think it's a good idea to consider
SEO itself early on. Dave is right that links will outweigh your code, but at the same time good code reduces your reliance on links to some degree and I don't know too many SEOs who are going to ignore what you're doing internally so might as well get it right from the start.