I am currently playing the entire Suikoden series on my PS3 and I ran into some severe difficulty when trying to transfer my SII data over to SIII because the PS3's internal memory card system will not allow for any PS1 data to be transferred onto a PS2 virtual card. As I have seen some folks on other forums expressing the same problem, I thought I would post the solution I worked out on here, in case anyone else is trying to play through this entire series on new hardware.
Firstly, you will need three things in addition to your SII data on a virtual card. You will need an actual PS2, a PS2 memory card, and you will need a PS3 memory card adapter.
After that, the process is reasonably simple.
1. Plug your memory card adapter with a PS2 memory card into the USB port on the PS3.
2. Copy your SII data from your virtual PS1 card over to the physical PS2 card in the adapter. (the software will allow a PS1 virtual transfer to a physical PS2 card, but not to a virtual one)
3. Remove your physical PS2 card from the adapter and plug it into the slot on your PS2 machine. Insert your copy of SIII.
4. When asked to load data upon starting a new game, select your SII virtual data from the PS2 physical card and transfer it.
5. Play through the intro sequence and save your data to the PS2 card at the first flame save point.
6. Remove the PS2 memory card with your fresh SIII data from your PS2 and plug it into your PS3 adapter.
7. Using the memory card utility, copy your new SIII data onto a virtual PS2 card in the PS3 and put the card in a virtual slot.
8. Continue playing from your initial save point and enjoy the 4 boosted characters and 2 theater scripts, despite having played through SII on your PS3 machine originally.
Hopefully someone besides me will find this process useful. I was initially quite frustrated when I discovered that the data wouldn't transfer, but this rather convoluted process seems to work just fine. Of course, if you don't have a PS2 and a memory card adapter handy, you'll have to decide if the few token 'benefits' of the transfer are worth getting your hands on the necessary tools, but at least now you know how to do so if you have the desire.