In my opinion, Tools like Cordova (Phonegap) and Titanium exemplify a continuously evolving Grey Area between Web App and Native Mobile App Development. But even with this said; I think it's important to understand the differences between the two and the pros and cons of each approach. I don't think you should wait 2-5 years to do a startup (do it now!) but if this is the case, then you should have more than enough time to research the differences and decide which route you want to go (or maybe you do both, who knows). The aspects that I would focus on are Product/UX and Distribution/Fatigue:
Product/UX would relate to the Products you want to build and the User Experience you want to deliver; Understanding how each environment impacts performance (or not), how the app is launched (or used), and how the app behaves in each environment. It really depends on what you want to build and how you want it to work. Is the App Lightweight or Heavy? Is the performance acceptable considering the UX you want to deliver? Should it be launched from the Home Screen, or is a Browser OK?
Distribution/Fatigue would relate to how you intend to distribute and maintain the App; Understanding your customer (or potential customer) base, how to reach them (distribution path / user acquisition), and being realistic about the time/resources necessary to support your distribution plan from a development perspective. It really depends on how you plan to distribute, and how much time/resources you have at your disposal. Do you want to reach everyone or a specific group? Can you maintain multiple instances of your client across multiple platforms?
The last thing I would note is the Platform Effect and how it might impact the Grey Area. I think it's important to note that each Mobile Platform maintains control over their platform, and thus (just like API based platforms) it is always possible that the rules get changed. I think this is important to note because it is possible that future changes may impact the acceptance/rejection of WebKit Wrapped Apps (aka the Grey Area).