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It could just be that your micro-SD card is very slow, and a faster one might help.
I am not sure exactly what activity you are measuring (sending metadata takes less than a second on my Glo, so we must be thinking of different things), but in general you should be able to work out how much of the time spent is due to Calibre and how much is due to the slow micro-SD card by closing and restarting Calibre with the device still plugged in and repeating the activity. The first time will be the time taken by Calibre plus the time Calibre spends waiting for the micro-SD card. The second time the files will be in the system cache and so the time should be almost entirely the time taken by Calibre. Subtract the second time from the first and you have the time taken by the micro-SD card.
E.g. I have about 1000 books on my Glo, Kobo database size is about 80MB, Calibre metadata is about 2.5MB. The first time I plug the device in it takes Calibre about 20 seconds to fetch data from the device. Close and restart Calibre with the device still plugged in and it only takes about 5 seconds, so I take it that Calibre is spending aout 15 seconds waiting on the micro-SD card. (I have a 8GB class 4 Sandisk card.)
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