I was wondering, which one would benefit me the most? I have as much time as I need to make a game engine and rapid development does not appeal to me. Unity3D is easy, but how much will mastering Unity3D gain to my knowledge of game development, compared to making a game engine?
Your question let assume that you want to gain knowledge in game development. As I understand it, you want to make games but don't really know what is the best for you.
Long story short: don't ever believe that you have "enough time" to make a game engine. This is a hard work. A very hard work. Depending of your type of game you have to master several specifics fields of knowledge.
If you want to learn how to make games Unity is a great tool for that. Thanks to it you will learn concepts very specific to video game development without having the pain to build your own tools, render engine, physics engine...
If you have "enough time" (which I'm not sure) to make your own engine, you surely have enough time to look at UnityEngine in order to make an opinion and see if it can be useful for you.