Interestingly, I find the best way to address a problem like this is to modify the research speed down to 10-15%. When I played default research setting, I was ramping up to super capable ships in no time and things like fleet doctrine/equipping meant little because if I had chosen wrong, I could research out an alternative tech and get it on ships in minimal time. By playing at 10-15% research, your equipping and doctrine choices actually have real weight because you stay in low-tech for quite awhile and if you happen to have chosen wrong, then you are in for some trouble. It also makes spoilers a lot more scary because they are going to out tech you for several decades at least - heck, standard NPRs will likely out tech you when you encounter them for the first time. Mess with the difficulty all you want, the research speed has been the way to go for me.