It's important that you think about the monetization side of things. There are far more flash game sites than unity or HTML 5 game sites. So unless you are funded upfront to make a HTML 5 or Unity based game, you might be limiting yourself a bit in terms of monetization.
If you are doing 3d, you can do it in either flash or Unity, although I'd say that Unity is probably the better choice. So to some degree, what type of game you are making is important in deciding.