Isn’t it about time for an update and some enhancements to this great feature? Some suggestions:

1. Change the default Preflight Profile to something realistic for quality printing. The absence of warnings is misleading, making people think that everything is fine.
2. Divide the check for “Protected fonts” into two categories: 1. Fonts which do not allow embedding in PDF, 2. Activated Adobe fonts (the existing behaviour of flagging Adobe fonts as “not allowed” causes a lot of confusion)
3. Change the wording “Transparency not allowed” to just “Transparency” Transparency is rarely a problem nowadays, though it is still good to check whether everything looks as expected.
4. Give users the option to choose which kinds of transparency they want to check for, and which not – or at least between opacity, effects and overprint applied in the Attributes Panel.
5. Give users the option to choose which kinds of bleed problems they want flagged, so they can decide if they want to include text frames (which are rarely a problem), lines, images and image frames. This would reduce the clutter that makes it all too easy to overlook something 
6. Add an option to include Ink Limit. Looking though hundreds of pages in Separations Preview is very time consuming, and errors are easily overlooked.
7. Make it possible to choose between the existing behaviour of zooming in on errors, and keeping the selected view. The same goes for when you are finding and replacing text an need to decide depending on the context. E.g., choosing to show a bleed error will invariable result in zooming so close that one cannot see what is happening and what can be done about it. The opposite is the case when checking large pages with lots of small images.
8. Allow users to set a limit to how much non-proportional scaling is acceptable, such as “show only deviations larger than 3%”.
9. Make it possible to tab through the error messages, to quickly see the Info. Or even better, add a column so one can see the values just beside the errors, instead of only in the Info window. My dream: Change the whole view to make it similar to the Links Panel, so you are free to sort errors by all kinds of criteria.
10. When checking for colour errors, give users the options to distinguish between seeing colour warnings from images, and from the document (RGB in images may be OK, but not in the document)
11. Make it possible to see the names of conditional text indicators which causes errors.
12. Make it possible to check for missing links in Illustrator files.
13. Make it possible to flag an error as being OK, and to save this info with the document.
14. This is probably asking the impossible: It would be really cool if by some artificial intelligence you could detect “looks like 100% Black but is not” in vector graphics. With live text and graphics in InDesign itself, at least you can add unnamed colors to get an idea of the suspects, and perhaps temporarily change them to spots in order to “trick” Preflight to find them. Detecting Registration color in graphics works fine, but there are so many other varieties of black made from all the four CMYK colors, such as C=83 M=67 Y=51 K=95, which can look very ugly in print when used on thin lines or small text, and also cause problems on large areas because of too high ink coverage. Again, the only way I know is going through the whole document with Black turned off in Separations Preview, and try to spot thin lines etc. which would be safer to print in pure Black, a rather time consuming process.
15. Bleed Hazard warnings should not depend on the document bleed settings, but only on the choices you make in Preflight options. Suppose my document setup has a bleed of 5 mm, and Preflight is set to minimum 3 mm, I will still get warnings about missing bleed for images which extend more than 3 mm outside the page margin.
16. Paragraph marks, spaces, tabs etc. should not be marked as overset text. Please change this so that only real missing text is listed.
17. Registration color is flagged even when it will not appear on print, like in backlists with cropped PDF’s of covers, or when illustrations are reused by placing print-ready pages from other books. Please change this so that only real problems are listed.