Well, other than capacity, the main reason to use a Microdrive instead of CF is in a write-intensive application. i.e. if you wanted to try and run Linux on top of WindowsCE or something bizarre like that. For most PDA applications, CF or SD will be just fine and will last many years.
[techno-babble incoming. may cause dizziness, heart palpatations or nausea in lay persons]
Remember, flash cards can tolerate a relatively limited number of erase/write cycles compared to magnetic media. Each block of flash ROM can only be erased and rewritten so many times (approximately 100,000 I believe) before it can't be written to any more.
100,000 erase/write cycles sounds like a lot, and it is a lot for simply storing data that isn't updated regularly (like application files, MP3 files, photos, etc...). For data that may have to be re-written several times a minute (like a swap partition in Linux), you'd fry a CF card in a few months of use.
Granted, magnetic media has a maximum number of erase/write cycles before it fails as well. But magnetic disk can handle on the order of 1,000,000,000 erase/write cycles or more before failure. You're more likely to lose data to magnetic migration or mechanical failure than you are to wearing out the ferrous coating.
FYI: Just a side note - remember the "Built-in Storage" on your PDA is flash memory, too. Frequently rewriting the data stored there will wear your on-board flash out eventually. But again, for things like applications or data that isn't going to be re-written regularly, it would take years to decades to trash the on-board storage.
