All jolly interesting to read, I am not sure we answered one of the questions posted...
Your laptop will almost certainly be I/O limited when it appears so slow down - that is you will be normally be waiting for disk reads/writes to occur (regardless of how much memory you have). Exactly how that I/O wait is triggered depends on what you are doing (which applications you run and what you do with them). That is almost impossible to predict on a laptop as the use would be so varied, and is impacted by the applications, their configuration, the size of RAM and size of paging files etc etc.
Why would you want the fine grained security of NTFS if you bought a home computer - had you purchased a laptop for business/corporate/office use they might have considered that you would connect it to a MS domain and hence want to make use of those security features when sharing data.
Most likely FAT32 was the easiest and most flexible filesystem image to dump on the disk for the vendor, and given that the sales channel you used was targetted at home use, as opposed to business/corporate network use, this is most likely the explanation as to why you found FAT32.
Unless you can describe an accurate set of use scenarios that represent how you are going to use your laptop (almost impossible to do) and then run parallel tests, one on NTFS and the other on FAT32, then you will have no idea which will actually perform best. But you asked why FAT32 (not just which was better) and the answer is almost certainly that it was easier for the vendor
I agree with the above that NTFS is always a better choice just for reliability. Can anyone remember the NT "convert" command to change the filesystem to NTFS? It's been 8 years since I used it....