It seems to me that a few things are needed:

1. Limiting the 'trial penalty' to 25% or so of the sentence 2. Banning pleas that involve dropping charges in exchange for pleading to others 3. Proper funding for public defenders

The first and second are to solve the problem that prosecutors overcharge and defence lawyers advise innocent clients to plead guilty rather than risk significant jail time fight bogus charges. This seems to be a common tactic by prosecutors in the US and it should simply be banned through these mechanisms.

Of course the other problem is that people can't defend themselves against bogus charges because the cost is ruinous, so proper funding for public defenders is important.