I think when you say innovation you mean sustaining innovation, which is where you build something that serves the most profitable section of the market, therefore motivating incumbents to copy you. When playing that game it's almost always a lose for the startup, unless you quickly sell out to an incumbent.
There are some situations where incumbents will be motivated to fight startups on low profit clients. Typically this is when you have an incumbent who's profitability comes from having a high volume of low profit customers. In cases like that, it's not likely you will get a foothold unnoticed.