Basically, will I make big gains quickly and then get stuck when trying to exert full control in the future?
In a word: yes.
In more words: it depends on what you want to do when you "exert full control". Some things are best left to plug-ins and some you might have to throw out and do yourself in the long run.
I was asked to modify and existing site that was all WP based with tons of crap on it. I did find a plug-in called exec-php which allowed me to easily separate the WP framework from the custom stuff that I needed to do.
There is definitely a learning curve and there are a few weird things that WP does.