However, let's not forget it's a tool and it's not going to last forever. Eventually, some other tools will flourish, embracing new technologies, new devices, new platforms, better languages, or just being cheaper or having an editor with all beautiful colors. Of course this doesn't mean you'll quit making games. This means you'll go through the painful path of learning new ways of doing the same old stuff. It's always been like this. Although there's no way to get rid of this learning curve, wouldn't it be nice to try and minimize the impact? Certainly you can't prepare yourself for an imaginary tool that doesn't exist yet, but you can do things that will help you in the future.
"Programmers who program "in" a language limit their thoughts to constructs that the language directly supports. If the language tools are primitive, the programmer's thoughts will also be primitive.I think this is true not only for languages, but for any means to an end. I'm not saying that Unity is primitive, but it's just a medium and thus it's limiting by its own nature. Knowledge and experience are never replaced but tools and technologies are, so I'd rather put technology at the service of knowledge and not the other way around.
Programmers who program "into" a language first decide what thoughts they want to express, and then they determine how to express those thoughts using the tools provided by their specific language."
(Steve McConnell - Code Complete)
In object-oriented programming, when some part of a program needs to interact with some other part, it's usually done in the most abstract way possible, normally through interfaces or abstract classes. A lot of the cool features found in OOP, if not all, stem from sheer common sense, so wouldn't it be wise to apply common sense for everything? My common sense dictates me that while coding into Unity, or whatever medium for that matter, I try at the same time to stay away from that medium as much as I can. I usually code as if I had to port my game to a different medium tomorrow, forcing me to separate medium-agnostic code from medium-dependent code, which in turn forces me to first think in medium-agnostic terms and thus not producing medium-dependent thoughts.
Following this premise, my common sense also tells me to not put all my code in scripts. Because not every piece of code needs to be a script. I regard scripts as if they were little wrappers encapsulating some medium-specific features, like manipulating some GameObject's transform, playing a sound, reading input, tweaking some camera's properties... you get the idea. I put the rest of the code in normal classes and make sure these classes don't reference medium-dependent assemblies. (In practice this is usually not feasible since you'll probably be using some of the medium's basic types for everything, like Unity's Vector3, but I like to think of them as coincidental dependencies)
But, why bother? Doing things like this will make you slightly slower, probably. Let's say it makes you 10% slower. If you look at the final product, it may seem you wasted 10% of your resources by doing it in a different way just for the sake of it, but it's not the case. Actually you've invested that amount in modeling, sharpening and polishing your own tools, like your way of approaching problems and the way of coming up with solutions. Not a waste at all. Even if Unity is here to stay forever.