Which Preflight Profile attribute(s) are you turning on in the Preflight panel? When I turn on Image Resolution in the IMAGES AND OBJECTS section, Adobe Illustrator .ai files are not tagged as low resolution.
Preflight settings in IMAGES AND OBJECTS are:
Colour Image Minimum Resolution is 290ppi
Greyscale Image Minimum Resolution is 290ppi
1-bit Image Minimum Resolution is 800ppi
It seems when I save Document Raster Effects settings to 300dpi in Illustrator and place them into InDesign in at a smaller size, Preflight tells me that the resolution is something ridiculous as 23ppi!
Weird thing is - older AI files do seem to be flagged as low-resolution (CS6 and back) - this just seems to be caused by new CC files. Even the ones with gradients and transparency.
I've checked everything I can possibly think of, and all my settings are the same. Even back-saving to older versions still brings up the same problems.
I have been using Adobe software for years, and like to think I can always find a solution. This never used to happen with Adobe Illustrator files before and I'm totally scratching my head!
I'm getting a totally different result from you with InDesign CC 2014 and an Illustrator CC 2014 file placed.
The Illustrator file is a simple vector with a drop shadow applied. Document Raster Effects is set at 300 ppi. I saved as an AI file and placed in the newest version of InDesign.
I made a preflight profile that only checked for Resolution (as shown). No errors were found:
Note that it is totally wrong to characterize EPS and AI files as vector files!!!!
In fact, EPS files may contain raster images as well as text and vector content. Virtually anything in PostScript can also be in EPS! In fact, Adobe Photoshop has EPS as one of the file formats to which you may save content (although not really recommended - it is a “legacy” format that doesn't support many new features.) It is also true that in Illustrator one may place raster images.
When placing EPS, PDF, or AI (in the case of AI, you are actually placing PDF), the content is internalized within InDesign. Thus, a low resolution image that happens to a component of an EPS, PDF, or AI file will in fact be characterized as low resolution by InDesign's Preflight.
Also note that transparency effects on vector or text items in Illustrator documents may cause raster images to be generated such as for drop shadows. The resolution of such raster images is controlled within Illustrator as an option. For publication purposes, you should always set that to at least 300dpi. A 72dpi transparency effect image is possibly what is triggering the message you are getting from InDesign Preflight.
Let us know what you actually find.