I understand there are some runtime implications but the vast majority of the "classes" created in my applications are instantiated once or only at startup. The memory usage and speed implications are negligible compared to the added maintainability.

In the grand scheme of all the allocation and computation taking place in my applications, these concerns are very far down the line.

Now, if you happen to be creating an application or framework that for some reason has to do a whole lot of allocating and might be meaningfully and measurably affected by such issues, then by all means use prototype "methods" when it will make a difference.

Personally, code clarity is much more important than making sure my application starts microseconds faster and allocates several bytes fewer per instance when there are only going to be ~10s of instances ever created.