Since flash memory has no moving parts, (other than zoom and focus), the battery lasts longer than HDD (or miniDV tape).
Since flash memory (and miniDV tape) is removable, in theory, you have unlimited recording capability limited to your power availablity - and the number of spare memory cards you have available. When you fill the hard drive in the HDD camcorder, you need to off load somewhere...
If the camcorder is broken, with flash memory (and miniDV tape), take the card (or tape) out and use another similar camcorder. Technically, the hard drive in the HDD camcorder is not user- removeable/serviceable.
If the camcorder is stolen, with flash memory (and miniDV tape), your video loss is limited to the card in the camcorder. With HDD camcorders, the video loss could be many hours of video not yet transferred.
HDD camcorders have issues with high altitude that flash memory (and miniDV tape) does not have.
HDD camcorders have issues high levels of prolonged vibration that flash memory (and minDV tape) does not have.
Consumer flash memory and HDD camcorders record to the same files formats - in the case of high definition, AVCHD (MTS files). These are very highly compressed - the newer consumer cams can stream at 24 mbps at highest quality, some models are limited to 17mbps - higher is better. MiniDV tape's HDV streams at 25mbps.
MiniDV tape continues to provide the cheapest $/gig storage when compared to flash memory or HDD formats.
When you don't re-use the tape, the miniDV tape that captured the video is the archive. How are you planning to archive the flash memory and hard disc drive video? (Remember, archive - not temporary backup.)
How are you planning to playback the finished high definition video project? With miniDV tape, your HDV-friendly video editor can export the finished project back to the camcorder and you can use the camcorder as a playback deck. Not so with other storage media. This limits you to having a BluRay burner on your computer (and playback with a BluRay player or PS3), rendering short clips of AVCD-encoded video to standard single layer or double layer DVDs (and playback with a BluRay player or PS3), or rendering video data files that stay in computer-readable format and connecting a computer to the HDTV with a VGA cable - or HDMI is your computer has that capability. Of course, you can always downsample to standard def and burn VOB-file regular DVDs for playback in regular DVD players - but the source of the high definition video is irrelevant.
Since you already found the flash memory based Canon HF-S series, your only other choice in your price range is the Canon HV40.
Your next set of questions should revolve around audio capture, use and availability of manual audio controls and editing hardware and software...
What camcorders in the $2,000-$3,000 range did you find? What digital video format do they save to?