This is a topic that I'm slightly uncomfortable about writing the “truth” as I see it. I shall put my cards on the table and say that as someone who designs and invents things, and loves to see progress in various ways, there is a big problem with start-up business and innovation.
The problem is fundamentally that innovation requires the breaking down of barriers. These are sometimes psychological barriers or red-tape barriers or the worst of all, inertia. For those who may not be familiar with Newton's first law, inertia (yes this is using it as a business metaphor) is the law of motion (which has now stood unchallenged for 200 years) that objects will carry on going in a certain direction and at a certain velocity unless there is a force to stop it or alter its direction.
Here on earth, the main force that appears to stop this rule is gravity. If you are a new business, the chances are that you may not have the resources to really make a significant impact to really alter the way (the inertia) in which people behave. I think that true innovation is possible for the start-up, though very difficult.
Thinking, for example, of the way in which James Dyson, who made the first bagless vacuum cleaner; it was an amazing achievement of courage and fighting against high odds. However, for every one who truly makes it, there will have been literally hundreds who will have gone bust in the process. Innovation is more suited to established businesses who can truly afford to bear the costs of altering the inertia of a way of doing things.
Getting patents on innovation is long term, expensive process that can easily defeat the short-term requirements of a business. Legal battles are not for the feint-hearted and you'd need to have a constitution of iron to get through this type of distraction.
A lot depends on your experience in such fields and how much money and time you've got to put into it. If however you are simply looking to protect a name (e.g. a brand name) then a trademark is comparitively very easy to attain.
A few years after one of my websites became reasonably successful, there were a few people who started using my web-address name in their keywords for their own site and on adwords (the Google paid-for advertising thing). This prompted me to spending about £500 on getting the name trade-marked (I'm sure it could be done cheaper too).
With the trademark, I could confidently send satisfyingly stroppy emails to all the cretins whom had tried to piggy-back on my site-name, reminding me of the indignant farmers' “Get aaarf myyy laaaaaand!!” rasping shouts, that I used to get when trying to play soccer on fields as a kid, ooh aaargh!