The way I see it when they were purchased, Jovetic was meant to be Aguero's backup and Negredo was meant to be Dzeko's backup . This is why we rarely see, Jovetic and Aguero together and Negredo and Dzeko together.
The problem is both Jovetic and Aguero have been injured for a good part of the season and when Negredo got injured we had no choice but to transition to play a single forward. Credit has to go to Dzeko also who carried it pretty well on his own. Add to this that we are no longer in CL, all the forwards are back to healthy and it's easy to see why Negredo's playing time has shrunk.
I think Pellegrini wants to play with two forwards, Aguero with Negredo and Dzeko with Jovetic. And ideally all forwards will probably be seeing similar amount of time on the pitch.
Inter's owner when asked about Dzeko was recently quoted saying: "I only announce the players that we sign, not the players that we dream about"
<a class="postlink" href="http://www.goal.com/en/news/10/italy/2014/04/29/4784130/zanetti-to-retire-this-summer-and-become-inter-director" onclick="window.open(this.href);return false;">http://www.goal.com/en/news/10/italy/20 ... r-director</a>
Which leads me to believe that Dzeko might actually be staying as well (but then again anything is possible, there is certainly interest which is likely to grow after WC).
edit: another interesting fact is Dzeko only has 30 more minutes played in the League games. So can't really complain that much considering he has been injured too.