Check with the universities you're planning to apply to, both in terms of the content of courses (what books they use, for example), and how easy it is to skip lower level classes. Normally, you would have the option to try and test into a higher level - whether that's with an internal test or whether they take the JLPT or similar into account depends. Either way, you want to skip the very beginner classes as they will be full of time-wasters and probably be quite slow.
It still might be worth it to you to take N3 (depending on how easy it is for you to get to the test site, etc). For example, it will at least give you some experience with taking JLPT under test conditions, so that you don't go into N2 blind. You might find it useful as feedback on where your weak points are.