At the very least, the inability for an alliance to declare a dead-ball when one is stuck within an opposing robot should be resolved. Either by allowing a "dead ball" to be declared in any robot, or by rendering a ball dead when prolonged possession by an opposing alliance has occurred.
Personally, I believe the initial possession should be limited to a foul , prolonged (5sec) possession should yield an additional technical foul and immediately declare the ball field debris (same handling as a popped ball).
See this:
http://www.thebluealliance.com/match/2014misou_qf3m1
Our (blue) robot has the Red ball bounce into our mechanism at 1:37 video time, our drivers are trying to clear the ball for the remainder of the match (the prolonged possession was not intentional, the drivers overlooked an easy solution of reversing the collector, and we struggled to load the over-inflated ball into our shooter).
Eventually (at 2:00 video time) the head ref signals for a new red ball to be put into play, however they fail to score the ball, and our alliance manages to overcome the 100pt penalty by just 2 points.