I do wish Bundler would simply be bundled into Ruby at this point; it's become so ingrained that there's no longer any reason to not make it a first-class citizen. The one big problem with Bundler is "bundle exec", which is required because project-local gems can conflict with system-wide gems. If all of Ruby honoured Bundler, we could let the Ruby runtime itself handle the gem isolation.
My main complaint about Bundler and RubyGems (and NPM for that matter) is that we're still unpacking packages with no good reason. RubyGems would be easier to deal with if you could just treat .gem files like Java does with JAR files. (The sore point is gems requiring compilation of binaries, but that's solvable.)
Actually, I have another complaint: Even after numerous security gaffes, gems still generally aren't signed.