Assuming you are going to take only one of the two domains, consider the following factors.
Is .com available for registration. If not then what is it going to cost you for acquiring .com. It won’t make business sense to acquire a .com version of the name if it costs, say more than your total project estimation.
2. Target audience
If you are targetting a particular country, then what is more popular in that particular country, .com or .net. If .net is what is popular, then its better to go with .net. I would also consider the cctld(.co.uk for uk, .us for us etc) before making a decision.
Some cool hacks are possible with .net domains. Eg: FindJobsOn.Net makes more sense than FindJobsOn.Com. Again this applies to each specific case as such.
4. Source of traffic
What source of traffic are you targetting? Type-ins, Search engines, Backlinks etc. If your major traffic source is type-in, better to get .com as people(especially in US) tend to type-in the .com name. If your major traffic source is from Search engines or Backlinks, depending on other factors you can choose either .com or .net.
Having said all, i want to look into some of my fellow domainers views
a. Majority of the traffic will go for .com if .net is developed site
Well this again depends on source of traffic. In most of the cases, “majority” of the traffic is not going to leak but only some part of the traffic. This is not that big a factor, if you are targeting traffic from Search engines and Backlinks.
b. If my .net becomes a hit, i will have to shell lot of money to get hold of .com
First of all, there is no need for you to go for .com name if your .net is already an established site. More people are getting smarter these days and making use of search engines to find the site compared with pure type-ins. Also if you are a die hard domainer who wants the .com version as well, you can think the other way. Lets say your .net has become a hit and if your name is a TM, then you have a better chance of getting hold of .com provided your TM is violated. Also in this case, .com owner can only dream of getting the big money from you as an enduser. So you might be in a good position to get the .com with the luxury of playing the wait game. Not many people would be willing to buy the .com which has a TM.