I personally don't mind the Deepspace Encounters (Enemy Signal Contacts) and accept them as part of the game. I figure that while traveling through space your might encounter the roaming Klingon or Romulan, and you need to avoid them by going around them. Dodging the Borg cubes in the B'tran cluster is not that hard - I get sucked in to combat once a week max. I kinda miss the danger I felt then I first started playing
What I would like to change is the ability to engage Enemy Signals that are lower than my current rank. Sometimes I feel like working towards an accolade (romulan for example), and none of them will engage me. It takes me ages to find an existing Contact to entre.