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When I took EE back in my college years, we actually looked into the physical layout of flash memory and saw exactly why larger chips will by definition have slower "seek" times (it's not technically a "seek", since there are no spinning platters or moving arms seeking out the proper sector, but the effect is identical). [Side note: This, along with the cost and relatively short lifespan of flash, is why it took so long to get from flash drives being so ubiquitous to SSDs becoming generally available.]
I'd elaborate on that now, but I can't remember the details. It was something about how each cell was addressed and accessed, and something about smaller numbers of cells ironically allowing more simultaneous access (i.e. read from/write to multiple cells at the exact same time).
Anyway, that being said, in my experience I've never noticed a significant difference, except that Windows seems to take longer to load up the directory in Explorer with larger drives (even if they have fewer files).