To pick up on what Zombimode said...

You have to choose what traits to breed for. If you emphasize small seeds, then you're not emphasizing taste or shelf-stability. If you emphasize taste, you're not emphasizing small seeds, and so on. Most wild fruits were at least somewhat selecting for taste because they wanted animals to pick them.

If you don't breed for taste, you'll end up with something like the modern strawberry, which looks good in the supermarket for a long time but doesn't taste nearly as good as it used to.