I'm kinda in the same boat as you. My first console was an NES and ever since then I always was attached to my very basic console controls with only a few buttons to push. I had a Gamboy for a while before the Xbox 360 finally came out and I got that. All my teenage years I've played 360 up until Arma 3 caught my attention and I got a laptop. My first year owning Arma 3, I sucked at playing because I hadn't played on M&K since I was a kid and my dad let me play Medal of Honor Allied Assault or Command and Conquer Renegade. Arma 3 was really bugged, I wasn't a fan of the difficulty (coming out of CoD and BF4 on 360), I wasn't familiar with M&K controls, and I didn't know anything about modding at the time so Arma lost its luster for a while and I went back to my 360.
It wasn't until I found the 506th that I actually got back into playing Arma again. I liked all the mods and new features that came in recent updates as well as some of the DLC content. I joined the 506th and learned about the roleplaying and realism experience. This all forced me to become more familiar with M&K than I used to be.
Now for me it just depends on the tempo of the game. Games such as Arma 3 and Left 4 Dead 2 are very high tempo games when you get into the thick of things and I like using the M&K to keep up snappy movements and customize my keybinding where I like them. However on games such as Far Cry 4, Metal Gear Solid V, GTA V, Skyrim and Fallout 4, I get my 360 controller and plug it into my computer because they're more simple games that I can play with only a controller and I like the slower, more fluid motions that the joystick of my controller provides allowing for a more subtle and smooth gameplay experience.