The matter of the fact is that the writers have dropped massive hints and clues for most of the 7 suspects. At least the ones we've seen a lot of, and I'm sure Heller will be dropping hints for Reede Smith and Thomas Mcallister in Series 6.

Here are some of the big hints we've seen already:

Bret Stiles:
-Gave Jane the location for Kristina Fry
-Described the release of stress as a "red cloud" to Van Pelt.

Bob Kirkland:
-Overall suspicious manner. Seen in the Limo for example.
-Killed Lennon, plus the "Do you recognise me?"
-Drank a Bloody Mary, the same drink Jane has three of on the anniversary of his family's murder.
-Similar voice.

Brett Partridge:
-Too much enthusiasm when dealing with RJ cases.
-The scene when PJ surprises him is mirrored with the Red John scene in "Red Sky at Night"
-Similar voice
-"Partridge" - it's connections to Blake

Gale Bertram:
-Reciting Blake's poetry.
-His mystery vacation while leaving the team without a license to work.

Ray Haffner:
-Right after it's revealed that RJ was a member of Visualize....Tad dah! Haffner is revealed to be a member of Visualize.

Even minor characters like Ellis Mars have had big hints dropped that they may be Red John, so it's really hard to know what's relevant when you have no evidence and it's purely theories.

Here are some questions that have been left unanswered:
How did Red John know about "Roll Tide" in Red Sky at Night? Was he at the date?

Why didn't Red John kill Bret Stiles if he knows information about Red John, and is willing to tell Jane some of it?

What did Bosco whisper in Jane's ear the moment before he died?

The answer to the last one has still been hidden away from us and may come into play at sometime. I'm just hoping the writers haven't thought we've forgotten about it.