I am in a similar situation where at the moment due to work and family I only get a short amount of practice in but I make sure I get those precious minutes daily without exception. Sometimes the wife doesn't understand and I help her to understand by explaining that some people may smoke a cig, some people may play a video game,cards etc for a few moments a night I chose to play my guitar and she is usually cool after that.

Now to answer your question specifically, what I do is work on a scale to improve my speed and I do chord switches that are giving me trouble. I am in the near future when I get my new guitar probably going to shelf the chord exercises and work mostly on my speed and accuracy doing licks and riffs. This in your case will depend on what kind of music you want to play. My focus is on heavy shredding with some rock stuff to. So isolate what you wanna do and focus on the exercises that hone the skills needed to play that style of music.